├── .ipynb_checkpoints └── ABFE_Gromacs__quantao_MD_Cloud_gmx_for_Justin__tutorial-checkpoint.ipynb ├── ABFE_Gromacs__quantao_MD_Cloud_gmx_for_Justin__tutorial.ipynb ├── FEP_by_NAMD_and_maestro.ipynb ├── IC50 to pIC50.ipynb ├── LICENSE ├── NAMD_3_0alpha8_Linux_x86_64_multicore_CUDA_SingleNode_tar_gz.ipynb ├── RBFE_sire_ligandswap_2.ipynb ├── README.md ├── Simple MD with OpenMM.ipynb ├── Simple MD with OpenMM_2.ipynb ├── Vina_PDB_self_dock.ipynb ├── charmm_gui_input_generator_based_namd_source_precompiled_CUDA_solution_md.ipynb ├── conda+rdkit+obabel.ipynb ├── conda-rdkit-smiles-draw_to_PNGs.ipynb ├── conda-rdkit-smiles-fragmentation-recap.ipynb ├── conda_rdkit_openmm_on_google_colab_modified_by_Tao.ipynb ├── convert smiles to sdf.ipynb ├── download_a_list_of_pdb_files_3.ipynb ├── gromacs_abf_run.sh ├── ipymol.ipynb ├── namd2.14-cuda-GPU-charmm-gui-with-Colab.ipynb ├── namd_charmm_gui_solution.csh ├── namd_charmm_gui_solution.sh ├── source_namd_compilation_for_relative_binding_free_energy_based_on_charmm_gui_input_generator.ipynb ├── 绝对结合自由能平衡+_eABF_二合一BFEE_1mq5_equlibratioin.ipynb ├── 随机森林.ipynb └── 随机森林_修订版本.ipynb /IC50 to pIC50.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "在构效关系模型的建立中，首先要把IC50数据转换为pIC50，这么做会促使实验者以对数方式设计实验区间，分析实验数据，而不是仅仅在算数尺度设计实验和分析数据。\n", 8 | "\n", 9 | "对于大多数生物应答系统，输入数据间隔为对数尺度时，才有可能会观测到反馈数据的不同；算数尺度的应答，将会带来大的误差风险或者无法观测到有效差异。因此在进行QSAR模型建立前，对于IC50,转换成pIC50是及其必要的。\n", 10 | "\n", 11 | "pIC50将更好的协助实验者正确评估自己的生物实验数据，特别是不至于过度夸大IC50的差异，如100 nM 与 300 nM 可能看起来差别为200 nM, 而从pIC50 角度，它们只相差0.48，属于同一级别的数据。\n", 12 | "\n", 13 | "将IC50 转换为pIC50 也提高了数据的可读性，正如最后几行python所示，通过简单的分类，实验者可快速通过在一个很小的区间内对该数据进行好坏的归类，而不必在原始的IC50所包含的从一到万的区间内进行区分，这将提高工作效率。" 14 | ] 15 | }, 16 | { 17 | "cell_type": "markdown", 18 | "metadata": {}, 19 | "source": [ 20 | "Covert IC50 from nanomolar to Molar, here I assume all the input IC50s are in namomolar, since this is most the case.\n", 21 | "首先我们把IC50从纳摩尔转换成单位为摩尔,转换关系为10的9次方" 22 | ] 23 | }, 24 | { 25 | "cell_type": "code", 26 | "execution_count": 109, 27 | "metadata": {}, 28 | "outputs": [ 29 | { 30 | "name": "stdout", 31 | "output_type": "stream", 32 | "text": [ 33 | "IC50_Molar: \n", 34 | "3e-07\n" 35 | ] 36 | } 37 | ], 38 | "source": [ 39 | "IC50_NanoMolar = 300\n", 40 | "\n", 41 | "IC50_Molar = IC50_NanoMolar / 1000000000\n", 42 | "\n", 43 | "print(\"IC50_Molar: \")\n", 44 | "print(IC50_Molar)" 45 | ] 46 | }, 47 | { 48 | "cell_type": "markdown", 49 | "metadata": {}, 50 | "source": [ 51 | "Then the next cell just put the IC50 in molar to its negative logarithm\n", 52 | "接下来只需取其负对数即可,不过需要先引入math函数" 53 | ] 54 | }, 55 | { 56 | "cell_type": "code", 57 | "execution_count": 36, 58 | "metadata": {}, 59 | "outputs": [], 60 | "source": [ 61 | "import math" 62 | ] 63 | }, 64 | { 65 | "cell_type": "code", 66 | "execution_count": 110, 67 | "metadata": {}, 68 | "outputs": [ 69 | { 70 | "name": "stdout", 71 | "output_type": "stream", 72 | "text": [ 73 | "6.5228787452803365\n" 74 | ] 75 | } 76 | ], 77 | "source": [ 78 | "pIC50 = -math.log (IC50_Molar,10) \n", 79 | "print(pIC50)" 80 | ] 81 | }, 82 | { 83 | "cell_type": "markdown", 84 | "metadata": {}, 85 | "source": [ 86 | "Now let's try to comment the bioactivity of this certain value of IC50, here I define pIC50 >= 7 good, pIC50 < 5 bad, and 5== 6.5:\n", 107 | " print(\"The bioactivity is good\")\n", 108 | "else:\n", 109 | " print(\"The bioactivity is medium\")\n", 110 | " " 111 | ] 112 | } 113 | ], 114 | "metadata": { 115 | "kernelspec": { 116 | "display_name": "Python 3", 117 | "language": "python", 118 | "name": "python3" 119 | }, 120 | "language_info": { 121 | "codemirror_mode": { 122 | "name": "ipython", 123 | "version": 3 124 | }, 125 | "file_extension": ".py", 126 | "mimetype": "text/x-python", 127 | "name": "python", 128 | "nbconvert_exporter": "python", 129 | "pygments_lexer": "ipython3", 130 | "version": "3.8.5" 131 | } 132 | }, 133 | "nbformat": 4, 134 | "nbformat_minor": 4 135 | } 136 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2021 quantaosun 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /NAMD_3_0alpha8_Linux_x86_64_multicore_CUDA_SingleNode_tar_gz.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "nbformat": 4, 3 | "nbformat_minor": 0, 4 | "metadata": { 5 | "colab": { 6 | "name": "NAMD_3.0alpha8_Linux-x86_64-multicore-CUDA-SingleNode.tar.gz.ipynb", 7 | "provenance": [], 8 | "authorship_tag": "ABX9TyOjvR4ockityDAiTZOt4MQb", 9 | "include_colab_link": true 10 | }, 11 | "kernelspec": { 12 | "name": "python3", 13 | "display_name": "Python 3" 14 | }, 15 | "language_info": { 16 | "name": "python" 17 | } 18 | }, 19 | "cells": [ 20 | { 21 | "cell_type": "markdown", 22 | "metadata": { 23 | "id": "view-in-github", 24 | "colab_type": "text" 25 | }, 26 | "source": [ 27 | "\"Open" 28 | ] 29 | }, 30 | { 31 | "cell_type": "code", 32 | "metadata": { 33 | "colab": { 34 | "base_uri": "https://localhost:8080/" 35 | }, 36 | "id": "3fOqdOAwOxo2", 37 | "outputId": "745cbcac-3d40-4303-ec23-8b628865deb6" 38 | }, 39 | "source": [ 40 | "from google.colab import drive\n", 41 | "drive.mount('/content/drive')" 42 | ], 43 | "execution_count": 1, 44 | "outputs": [ 45 | { 46 | "output_type": "stream", 47 | "text": [ 48 | "Mounted at /content/drive\n" 49 | ], 50 | "name": "stdout" 51 | } 52 | ] 53 | }, 54 | { 55 | "cell_type": "code", 56 | "metadata": { 57 | "id": "XC6NXjzGOueA" 58 | }, 59 | "source": [ 60 | "!mkdir /content/drive/MyDrive/2021-07-12" 61 | ], 62 | "execution_count": 2, 63 | "outputs": [] 64 | }, 65 | { 66 | "cell_type": "code", 67 | "metadata": { 68 | "colab": { 69 | "base_uri": "https://localhost:8080/" 70 | }, 71 | "id": "ssqkLZchPNuW", 72 | "outputId": "808abcb2-4a88-4c49-d3b1-ced1160f4853" 73 | }, 74 | "source": [ 75 | "!wget https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/download/NAMD_3.0alpha8_Linux-x86_64-multicore-CUDA-SingleNode.tar.gz" 76 | ], 77 | "execution_count": 3, 78 | "outputs": [ 79 | { 80 | "output_type": "stream", 81 | "text": [ 82 | "--2021-07-12 05:47:09-- https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/download/NAMD_3.0alpha8_Linux-x86_64-multicore-CUDA-SingleNode.tar.gz\n", 83 | "Resolving www.ks.uiuc.edu (www.ks.uiuc.edu)... 130.126.120.43\n", 84 | "Connecting to www.ks.uiuc.edu (www.ks.uiuc.edu)|130.126.120.43|:443... connected.\n", 85 | "HTTP request sent, awaiting response... 200 OK\n", 86 | "Length: 217898714 (208M) [application/x-gzip]\n", 87 | "Saving to: ‘NAMD_3.0alpha8_Linux-x86_64-multicore-CUDA-SingleNode.tar.gz’\n", 88 | "\n", 89 | "NAMD_3.0alpha8_Linu 100%[===================>] 207.80M 17.2MB/s in 13s \n", 90 | "\n", 91 | "2021-07-12 05:47:27 (15.5 MB/s) - ‘NAMD_3.0alpha8_Linux-x86_64-multicore-CUDA-SingleNode.tar.gz’ saved [217898714/217898714]\n", 92 | "\n" 93 | ], 94 | "name": "stdout" 95 | } 96 | ] 97 | }, 98 | { 99 | "cell_type": "code", 100 | "metadata": { 101 | "id": "zE9k2CD4Qmzd" 102 | }, 103 | "source": [ 104 | "!cp NAMD_3.0alpha8_Linux-x86_64-multicore-CUDA-SingleNode.tar.gz /content/drive/MyDrive/2021-07-12" 105 | ], 106 | "execution_count": 4, 107 | "outputs": [] 108 | }, 109 | { 110 | "cell_type": "code", 111 | "metadata": { 112 | "id": "ho8mGP1QPN2E" 113 | }, 114 | "source": [ 115 | "!cp need_to_run_solvent.tar.gz /content/drive/MyDrive/2021-07-12" 116 | ], 117 | "execution_count": 5, 118 | "outputs": [] 119 | }, 120 | { 121 | "cell_type": "code", 122 | "metadata": { 123 | "colab": { 124 | "base_uri": "https://localhost:8080/" 125 | }, 126 | "id": "2W2yZQzYQ_DN", 127 | "outputId": "7dc27a89-5243-40bb-fad0-c28b2243a227" 128 | }, 129 | "source": [ 130 | "%cd drive/MyDrive/2021-07-12" 131 | ], 132 | "execution_count": 7, 133 | "outputs": [ 134 | { 135 | "output_type": "stream", 136 | "text": [ 137 | "/content/drive/MyDrive/2021-07-12\n" 138 | ], 139 | "name": "stdout" 140 | } 141 | ] 142 | }, 143 | { 144 | "cell_type": "code", 145 | "metadata": { 146 | "id": "wa-VmXRVQ_-W" 147 | }, 148 | "source": [ 149 | "!tar -xvf NAMD_3.0alpha8_Linux-x86_64-multicore-CUDA-SingleNode.tar.gz" 150 | ], 151 | "execution_count": null, 152 | "outputs": [] 153 | }, 154 | { 155 | "cell_type": "code", 156 | "metadata": { 157 | "id": "xm4sHsnQROmF" 158 | }, 159 | "source": [ 160 | "!tar -xvf need_to_run_solvent.tar.gz" 161 | ], 162 | "execution_count": null, 163 | "outputs": [] 164 | }, 165 | { 166 | "cell_type": "code", 167 | "metadata": { 168 | "colab": { 169 | "base_uri": "https://localhost:8080/" 170 | }, 171 | "id": "lvtZVsnbRAEM", 172 | "outputId": "0fc6d200-e87c-4027-be0b-563e92c3dfb0" 173 | }, 174 | "source": [ 175 | "%cd /content/drive/MyDrive/2021-07-12/files_from_Feprepare/complex/complex-input-files/" 176 | ], 177 | "execution_count": 13, 178 | "outputs": [ 179 | { 180 | "output_type": "stream", 181 | "text": [ 182 | "/content/drive/MyDrive/2021-07-12/files_from_Feprepare/complex/complex-input-files\n" 183 | ], 184 | "name": "stdout" 185 | } 186 | ] 187 | }, 188 | { 189 | "cell_type": "markdown", 190 | "metadata": { 191 | "id": "HxKt5_wpS55f" 192 | }, 193 | "source": [ 194 | "Double check where is namd3 /content/drive/MyDrive/2021-07-12/NAMD_3.0alpha8_Linux-x86_64-multicore-CUDA/namd3" 195 | ] 196 | }, 197 | { 198 | "cell_type": "code", 199 | "metadata": { 200 | "colab": { 201 | "base_uri": "https://localhost:8080/" 202 | }, 203 | "id": "Rb_brthPQ_F_", 204 | "outputId": "5724b4b7-d087-4553-8df9-63107715633d" 205 | }, 206 | "source": [ 207 | "!" 208 | ], 209 | "execution_count": 16, 210 | "outputs": [ 211 | { 212 | "output_type": "stream", 213 | "text": [ 214 | "NVIDIA-SMI has failed because it couldn't communicate with the NVIDIA driver. Make sure that the latest NVIDIA driver is installed and running.\n", 215 | "\n" 216 | ], 217 | "name": "stdout" 218 | } 219 | ] 220 | }, 221 | { 222 | "cell_type": "code", 223 | "metadata": { 224 | "id": "AvbEfkKdQ_IW" 225 | }, 226 | "source": [ 227 | "" 228 | ], 229 | "execution_count": null, 230 | "outputs": [] 231 | } 232 | ] 233 | } -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | # notebook 3 | 4 | Note, for the notebook called “smina” docking, I just uploaded it here for my convenience when I need it since I am bad at managing files, I do not have any credit on this notebook at all, you should visit https://www.linkedin.com/pulse/using-google-colab-protein-ligand-docking-leela-sriram-dodda for its original link. 5 | 6 | If you can't get access to run.sh and analysis python script when using ABFE notebook, you may want to download it here 7 | 8 | https://qutesun.ml/post18.html 9 | 10 | 19/04/2021 11 | 12 | ----------------------------------------------------------------------- 13 | This is mainly for my purpose of doing molecular modeling, so there might be some Chinese inside the notebook 14 | if you can't understand that, you could write an email to quantaosun@gmail.com， potentially, I may be able to provide all English versions. 15 | 16 | Many of the codes inside the notebooks are other people's brilliant ideas which I just borrowed from them, I have tried to claim all possible sources where they come from either in English or in Chinese, in most cases you can get to the source by a URL link. 17 | 18 | The purpose of my notebooks is similar to many others, that is to democratize the wall of doing molecular modeling, reduce the cost of drug design and make people's life easier. 19 | 20 | The format may be not ideal, I will continue to improve that part. 21 | 22 | for the conda_rdkit_openmm_on_google_colab_modified_by_Tao.ipynb, you may want to use it with the following two links open in your browse 23 | https://github.com/openmm/openmm/blob/master/examples/input.pdb 24 | http://docs.openmm.org/latest/userguide/application.html#a-first-example 25 | 26 | for the ABFE which is to calculate the absolute free energy of a protein and a ligand, you may want to use it with these two links open 27 | http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016 28 | http://www.mdtutorials.com/gmx/complex/index.html 29 | Note that the ABFE needs quite a lot of computer resources, you may want to split your job into several sub-jobs. 30 | 31 | for the RBFE which is to calculate the relative free energy of two ligands, you may want to use it with the links below, 32 | https://siremol.org/tutorials/ligandswap/README.html (2021-04-18) 33 | 34 | For my FEP_by_NAMD notebook, you could head to have a look at my blog as well 35 | https://qutesun.ml/post6.html 2021-04-21 36 | 37 | For the Namd-charmm GUI notebook, it is derived from a youtube channel, which I will attach the link soon. 2021-04-21 38 | 39 | For the ipymol notebook, it is copied from another source which I list inside the notebook. 2021-04-29 40 | 41 | The job control bash script "gromacs_abf_run.sh" was added for The ABFE ipynb for gromacs simulation, gpu command improved. 42 | Two "namd_charm_gui_solution_md.csh/sh" files added, for the purpose of doing a normal protein-ligand simulation, based on the input generator of Charmm GUI. The coreponding workflow is not provided here, so you should go to Charmm GUI and read how to do a proper solution simulation. But why there are two script in csh, and sh respectively ? Well, the csh one is the default one come with Charmm GUI, it is handy to be used on google colab, but for my personal use, I sometime need to run the job on some other clound platform that I can't install a proper csh shell, so the bash/sh version is provided here for that purpose. If you want to know more about how to convert the csh script to a bash script, you might want to visit my site https://quantaosun.github.io/post23.html 2021-07-07 43 | 44 | 45 | Quantao 46 | 47 | quantaosun@gmail.com 48 | -------------------------------------------------------------------------------- /Simple MD with OpenMM.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "nbformat": 4, 3 | "nbformat_minor": 0, 4 | "metadata": { 5 | "colab": { 6 | "name": "最简约的蛋白质动力学模拟.ipynb", 7 | "provenance": [], 8 | "authorship_tag": "ABX9TyMDibX9nEMTo8d3Z2mr6jKx", 9 | "include_colab_link": true 10 | }, 11 | "kernelspec": { 12 | "name": "python3", 13 | "display_name": "Python 3" 14 | }, 15 | "language_info": { 16 | "name": "python" 17 | }, 18 | "accelerator": "GPU" 19 | }, 20 | "cells": [ 21 | { 22 | "cell_type": "markdown", 23 | "metadata": { 24 | "id": "view-in-github", 25 | "colab_type": "text" 26 | }, 27 | "source": [ 28 | "\"Open" 29 | ] 30 | }, 31 | { 32 | "cell_type": "code", 33 | "metadata": { 34 | "colab": { 35 | "base_uri": "https://localhost:8080/" 36 | }, 37 | "id": "x6iPrchOkbRt", 38 | "outputId": "7f3a47c2-a263-45f1-be37-b6965bbc6695" 39 | }, 40 | "source": [ 41 | "! wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh\n", 42 | "! chmod +x Miniconda3-py37_4.8.2-Linux-x86_64.sh\n", 43 | "! bash ./Miniconda3-py37_4.8.2-Linux-x86_64.sh -b -f -p /usr/local\n", 44 | "#! conda install -c rdkit rdkit -y\n", 45 | "import sys\n", 46 | "sys.path.append('/usr/local/lib/python3.7/site-packages/')" 47 | ], 48 | "execution_count": 1, 49 | "outputs": [ 50 | { 51 | "output_type": "stream", 52 | "name": "stdout", 53 | "text": [ 54 | "--2021-09-20 14:51:02-- https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh\n", 55 | "Resolving repo.anaconda.com (repo.anaconda.com)... 104.16.130.3, 104.16.131.3, 2606:4700::6810:8203, ...\n", 56 | "Connecting to repo.anaconda.com (repo.anaconda.com)|104.16.130.3|:443... connected.\n", 57 | "HTTP request sent, awaiting response... 200 OK\n", 58 | "Length: 85055499 (81M) [application/x-sh]\n", 59 | "Saving to: ‘Miniconda3-py37_4.8.2-Linux-x86_64.sh.1’\n", 60 | "\n", 61 | "Miniconda3-py37_4.8 100%[===================>] 81.12M 188MB/s in 0.4s \n", 62 | "\n", 63 | "2021-09-20 14:51:03 (188 MB/s) - ‘Miniconda3-py37_4.8.2-Linux-x86_64.sh.1’ saved [85055499/85055499]\n", 64 | "\n", 65 | "PREFIX=/usr/local\n", 66 | "Unpacking payload ...\n", 67 | "Collecting package metadata (current_repodata.json): - \b\b\\ \b\bdone\n", 68 | "Solving environment: / \b\b- \b\b\\ \b\b| \b\b/ \b\bfailed with initial frozen solve. Retrying with flexible solve.\n", 69 | "Solving environment: \\ \b\b| \b\b/ \b\b- \b\b\\ \b\bfailed with repodata from current_repodata.json, will retry with next repodata source.\n", 70 | "Collecting package metadata (repodata.json): / \b\bdone\n", 71 | "Solving environment: \\ \b\b| \b\b/ \b\b- \b\b\\ \b\bfailed with initial frozen solve. Retrying with flexible solve.\n", 72 | "Solving environment: / \b\b- \b\b\\ \b\b| \b\b/ \n", 73 | "Found conflicts! Looking for incompatible packages.\n", 74 | "This can take several minutes. Press CTRL-C to abort.\n", 75 | "\b\bfailed\n", 76 | "\n", 77 | "# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<\n", 78 | "\n", 79 | " Traceback (most recent call last):\n", 80 | " File \"site-packages/conda/cli/install.py\", line 265, in install\n", 81 | " File \"site-packages/conda/core/solve.py\", line 117, in solve_for_transaction\n", 82 | " File \"site-packages/conda/core/solve.py\", line 158, in solve_for_diff\n", 83 | " File \"site-packages/conda/core/solve.py\", line 281, in solve_final_state\n", 84 | " File \"site-packages/conda/common/io.py\", line 88, in decorated\n", 85 | " File \"site-packages/conda/core/solve.py\", line 808, in _run_sat\n", 86 | " File \"site-packages/conda/common/io.py\", line 88, in decorated\n", 87 | " File \"site-packages/conda/resolve.py\", line 1316, in solve\n", 88 | " conda.exceptions.UnsatisfiableError: \n", 89 | " Did not find conflicting dependencies. If you would like to know which\n", 90 | " packages conflict ensure that you have enabled unsatisfiable hints.\n", 91 | " \n", 92 | " conda config --set unsatisfiable_hints True\n", 93 | " \n", 94 | " \n", 95 | " During handling of the above exception, another exception occurred:\n", 96 | " \n", 97 | " Traceback (most recent call last):\n", 98 | " File \"site-packages/conda/exceptions.py\", line 1079, in __call__\n", 99 | " File \"site-packages/conda/cli/main.py\", line 84, in _main\n", 100 | " File \"site-packages/conda/cli/conda_argparse.py\", line 82, in do_call\n", 101 | " File \"site-packages/conda/cli/main_install.py\", line 20, in execute\n", 102 | " File \"site-packages/conda/cli/install.py\", line 299, in install\n", 103 | " File \"site-packages/conda/core/solve.py\", line 117, in solve_for_transaction\n", 104 | " File \"site-packages/conda/core/solve.py\", line 158, in solve_for_diff\n", 105 | " File \"site-packages/conda/core/solve.py\", line 281, in solve_final_state\n", 106 | " File \"site-packages/conda/common/io.py\", line 88, in decorated\n", 107 | " File \"site-packages/conda/core/solve.py\", line 808, in _run_sat\n", 108 | " File \"site-packages/conda/common/io.py\", line 88, in decorated\n", 109 | " File \"site-packages/conda/resolve.py\", line 1318, in solve\n", 110 | " File \"site-packages/conda/resolve.py\", line 347, in find_conflicts\n", 111 | " File \"site-packages/conda/resolve.py\", line 507, in build_conflict_map\n", 112 | " File \"site-packages/conda/resolve.py\", line 369, in breadth_first_search_for_dep_graph\n", 113 | " File \"site-packages/conda/models/match_spec.py\", line 481, in union\n", 114 | " File \"site-packages/conda/models/match_spec.py\", line 475, in merge\n", 115 | " File \"site-packages/conda/models/match_spec.py\", line 475, in \n", 116 | " File \"site-packages/conda/models/match_spec.py\", line 502, in _merge\n", 117 | " File \"site-packages/conda/models/match_spec.py\", line 764, in union\n", 118 | " TypeError: sequence item 0: expected str instance, Channel found\n", 119 | "\n", 120 | "`$ /usr/local/conda.exe install --offline --file /usr/local/pkgs/env.txt -yp /usr/local`\n", 121 | "\n", 122 | " environment variables:\n", 123 | " CIO_TEST=\n", 124 | " CONDA_CHANNELS=https://repo.anaconda.com/pkgs/main,https://repo.anaconda.com/pkgs/mai\n", 125 | " n,https://repo.anaconda.com/pkgs/r,https://repo.anaconda.com/pkgs/pro\n", 126 | "CONDA_EXTRA_SAFETY_CHECKS=no\n", 127 | " CONDA_PKGS_DIRS=/usr/local/pkgs\n", 128 | " CONDA_ROLLBACK_ENABLED=no\n", 129 | " CONDA_ROOT=/tmp/_MEIskfMGr\n", 130 | " CONDA_SAFETY_CHECKS=disabled\n", 131 | " LD_LIBRARY_PATH=/tmp/_MEIskfMGr\n", 132 | " LIBRARY_PATH=/usr/local/cuda/lib64/stubs\n", 133 | " OLD_LD_LIBRARY_PATH=/usr/lib64-nvidia\n", 134 | " PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/b\n", 135 | " in:/usr/sbin:/usr/bin:/sbin:/bin:/tools/node/bin:/tools/google-cloud-\n", 136 | " sdk/bin:/opt/bin\n", 137 | " PYTHONPATH=/env/python\n", 138 | " PYTHONWARNINGS=ignore:::pip._internal.cli.base_command\n", 139 | " REQUESTS_CA_BUNDLE=\n", 140 | " SSL_CERT_FILE=/tmp/_MEIskfMGr/certifi/cacert.pem\n", 141 | "\n", 142 | " active environment : None\n", 143 | " user config file : /root/.condarc\n", 144 | " populated config files : \n", 145 | " conda version : 4.8.2\n", 146 | " conda-build version : not installed\n", 147 | " python version : 3.7.6.final.0\n", 148 | " virtual packages : __cuda=11.4\n", 149 | " __glibc=2.27\n", 150 | " base environment : /tmp/_MEIskfMGr (read only)\n", 151 | " channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 (offline)\n", 152 | " https://repo.anaconda.com/pkgs/main/noarch (offline)\n", 153 | " https://repo.anaconda.com/pkgs/r/linux-64 (offline)\n", 154 | " https://repo.anaconda.com/pkgs/r/noarch (offline)\n", 155 | " https://repo.anaconda.com/pkgs/pro/linux-64 (offline)\n", 156 | " https://repo.anaconda.com/pkgs/pro/noarch (offline)\n", 157 | " package cache : /usr/local/pkgs\n", 158 | " envs directories : /root/.conda/envs\n", 159 | " /tmp/_MEIskfMGr/envs\n", 160 | " platform : linux-64\n", 161 | " user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.6 Linux/5.4.104+ ubuntu/18.04.5 glibc/2.27\n", 162 | " UID:GID : 0:0\n", 163 | " netrc file : None\n", 164 | " offline mode : True\n", 165 | "\n", 166 | "\n", 167 | "An unexpected error has occurred. Conda has prepared the above report.\n", 168 | "\n", 169 | "Upload successful.\n" 170 | ] 171 | } 172 | ] 173 | }, 174 | { 175 | "cell_type": "code", 176 | "metadata": { 177 | "colab": { 178 | "base_uri": "https://localhost:8080/" 179 | }, 180 | "id": "zc9QbRO7kbhb", 181 | "outputId": "0203d12c-e20f-4a39-ca6f-756be3a13c90" 182 | }, 183 | "source": [ 184 | "!conda install -c conda-forge openmm" 185 | ], 186 | "execution_count": 2, 187 | "outputs": [ 188 | { 189 | "output_type": "stream", 190 | "name": "stdout", 191 | "text": [ 192 | "Collecting package metadata (current_repodata.json): - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\bdone\n", 193 | "Solving environment: \\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\bdone\n", 194 | "\n", 195 | "# All requested packages already installed.\n", 196 | "\n" 197 | ] 198 | } 199 | ] 200 | }, 201 | { 202 | "cell_type": "code", 203 | "metadata": { 204 | "colab": { 205 | "base_uri": "https://localhost:8080/" 206 | }, 207 | "id": "TY2b9N3jl2Uw", 208 | "outputId": "ba151113-cce3-4473-efc1-6dd0546f5eac" 209 | }, 210 | "source": [ 211 | "!conda install -c conda-forge pdbfixer" 212 | ], 213 | "execution_count": 3, 214 | "outputs": [ 215 | { 216 | "output_type": "stream", 217 | "name": "stdout", 218 | "text": [ 219 | "Collecting package metadata (current_repodata.json): - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\bdone\n", 220 | "Solving environment: | \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\bdone\n", 221 | "\n", 222 | "# All requested packages already installed.\n", 223 | "\n" 224 | ] 225 | } 226 | ] 227 | }, 228 | { 229 | "cell_type": "code", 230 | "metadata": { 231 | "colab": { 232 | "base_uri": "https://localhost:8080/" 233 | }, 234 | "id": "NG8-Mi_zoelD", 235 | "outputId": "0eab2a3f-8e34-4432-c7cd-e2ea77a6635c" 236 | }, 237 | "source": [ 238 | "!pdbfixer --help" 239 | ], 240 | "execution_count": 4, 241 | "outputs": [ 242 | { 243 | "output_type": "stream", 244 | "name": "stdout", 245 | "text": [ 246 | "Usage: pdbfixer\n", 247 | " pdbfixer filename [options] \n", 248 | "\n", 249 | "When run with no arguments, it launches the user interface. If any arguments are specified, it runs in command line mode.\n", 250 | "\n", 251 | "Options:\n", 252 | " -h, --help show this help message and exit\n", 253 | " --pdbid=PDBID PDB id to retrieve from RCSB [default: None]\n", 254 | " --url=URL URL to retrieve PDB from [default: None]\n", 255 | " --output=FILENAME output pdb file [default: output.pdb]\n", 256 | " --add-atoms=ATOMS which missing atoms to add: all, heavy, hydrogen, or\n", 257 | " none [default: all]\n", 258 | " --keep-heterogens=OPTION\n", 259 | " which heterogens to keep: all, water, or none\n", 260 | " [default: all]\n", 261 | " --replace-nonstandard\n", 262 | " replace nonstandard residues with standard equivalents\n", 263 | " --add-residues add missing residues\n", 264 | " --water-box=X Y Z add a water box. The value is the box dimensions in nm\n", 265 | " [example: --water-box=2.5 2.4 3.0]\n", 266 | " --ph=PH the pH to use for adding missing hydrogens [default:\n", 267 | " 7.0]\n", 268 | " --positive-ion=ION positive ion to include in the water box: Cs+, K+,\n", 269 | " Li+, Na+, or Rb+ [default: Na+]\n", 270 | " --negative-ion=ION negative ion to include in the water box: Cl-, Br-,\n", 271 | " F-, or I- [default: Cl-]\n", 272 | " --ionic-strength=STRENGTH\n", 273 | " molar concentration of ions to add to the water box\n", 274 | " [default: 0.0]\n", 275 | " --verbose Print verbose output\n" 276 | ] 277 | } 278 | ] 279 | }, 280 | { 281 | "cell_type": "code", 282 | "metadata": { 283 | "colab": { 284 | "base_uri": "https://localhost:8080/" 285 | }, 286 | "id": "7fXgmwd8phqM", 287 | "outputId": "258a9a5f-f444-472a-a7f1-de05bd4cd50a" 288 | }, 289 | "source": [ 290 | "!pdbfixer --pdbid=3htb --output=myfile.pdb --add-residues " 291 | ], 292 | "execution_count": 5, 293 | "outputs": [ 294 | { 295 | "output_type": "stream", 296 | "name": "stdout", 297 | "text": [ 298 | "Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.\n" 299 | ] 300 | } 301 | ] 302 | }, 303 | { 304 | "cell_type": "code", 305 | "metadata": { 306 | "colab": { 307 | "base_uri": "https://localhost:8080/" 308 | }, 309 | "id": "x8M_pSlsl5g6", 310 | "outputId": "86694887-5558-4c57-b07d-986d03b5a57d" 311 | }, 312 | "source": [ 313 | "from pdbfixer import PDBFixer\n", 314 | "from simtk.openmm.app import PDBFile\n", 315 | "fixer = PDBFixer(filename='myfile.pdb')\n", 316 | "fixer.findMissingResidues()\n", 317 | "fixer.findNonstandardResidues()\n", 318 | "fixer.replaceNonstandardResidues()\n", 319 | "fixer.removeHeterogens(True)\n", 320 | "fixer.findMissingAtoms()\n", 321 | "fixer.addMissingAtoms()\n", 322 | "fixer.addMissingHydrogens(7.0)\n", 323 | "fixer.addSolvent(fixer.topology.getUnitCellDimensions())\n", 324 | "PDBFile.writeFile(fixer.topology, fixer.positions, open('input.pdb', 'w'))" 325 | ], 326 | "execution_count": 6, 327 | "outputs": [ 328 | { 329 | "output_type": "stream", 330 | "name": "stderr", 331 | "text": [ 332 | "Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.\n" 333 | ] 334 | } 335 | ] 336 | }, 337 | { 338 | "cell_type": "code", 339 | "metadata": { 340 | "colab": { 341 | "base_uri": "https://localhost:8080/" 342 | }, 343 | "id": "RJpJNOkzkbqu", 344 | "outputId": "77123a0d-c726-4555-a9a9-6a0594a02f11" 345 | }, 346 | "source": [ 347 | "from simtk.openmm.app import *\n", 348 | "from simtk.openmm import *\n", 349 | "from simtk.unit import *\n", 350 | "from sys import stdout\n", 351 | "\n", 352 | "pdb = PDBFile('input.pdb')\n", 353 | "forcefield = ForceField('amber99sb.xml', 'tip3p.xml')\n", 354 | "system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)\n", 355 | "integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)\n", 356 | "simulation = Simulation(pdb.topology, system, integrator)\n", 357 | "simulation.context.setPositions(pdb.positions)\n", 358 | "simulation.minimizeEnergy()\n", 359 | "simulation.reporters.append(PDBReporter('output.pdb', 1000))\n", 360 | "simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, potentialEnergy=True, temperature=True))\n", 361 | "simulation.step(100000)" 362 | ], 363 | "execution_count": 8, 364 | "outputs": [ 365 | { 366 | "output_type": "stream", 367 | "name": "stdout", 368 | "text": [ 369 | "#\"Step\",\"Potential Energy (kJ/mole)\",\"Temperature (K)\"\n", 370 | "1000,-392594.3403185059,250.43010649261626\n", 371 | "2000,-374818.9653185059,286.04927585047625\n", 372 | "3000,-369570.4653185059,297.3358102460518\n", 373 | "4000,-367965.2153185059,298.5230279826559\n", 374 | "5000,-367726.3403185059,298.0861061138377\n", 375 | "6000,-367040.4653185059,303.4847113506316\n", 376 | "7000,-367217.7153185059,300.5504198698757\n", 377 | "8000,-367943.7153185059,299.0864990635316\n", 378 | "9000,-367351.9653185059,297.5111558417348\n", 379 | "10000,-368190.2153185059,300.68008923547285\n", 380 | "11000,-367534.7153185059,300.1938013554846\n", 381 | "12000,-368215.7153185059,303.6503206924139\n", 382 | "13000,-366749.7153185059,300.0202958792206\n", 383 | "14000,-367688.2153185059,301.93414694370864\n", 384 | "15000,-367450.4653185059,298.9430327444774\n", 385 | "16000,-367010.2153185059,300.3396310137783\n", 386 | "17000,-368046.4653185059,299.67331932959956\n", 387 | "18000,-368102.4653185059,299.8267552807141\n", 388 | "19000,-368654.9653185059,300.4488057766935\n", 389 | "20000,-369003.2153185059,298.80051717174246\n", 390 | "21000,-367499.9653185059,295.4399174461358\n", 391 | "22000,-368794.5903185059,297.27688814262183\n", 392 | "23000,-366962.4653185059,299.3492415660463\n", 393 | "24000,-367822.0903185059,297.9970734545808\n", 394 | "25000,-366094.7153185059,298.0434201425909\n", 395 | "26000,-366452.9653185059,299.1511148715015\n", 396 | "27000,-367102.4653185059,299.12008926631637\n", 397 | "28000,-368265.9653185059,298.32965484243374\n", 398 | "29000,-368489.5903185059,298.24051271907945\n", 399 | "30000,-367390.9653185059,300.25597452527194\n", 400 | "31000,-366807.7153185059,299.389764644477\n", 401 | "32000,-366559.7153185059,299.17758701890176\n", 402 | "33000,-366497.9653185059,298.8771361613992\n", 403 | "34000,-366726.7153185059,296.7283406463203\n", 404 | "35000,-367963.4653185059,298.414302909497\n", 405 | "36000,-367692.0903185059,301.50788017675256\n", 406 | "37000,-367653.8403185059,302.5125280572825\n", 407 | "38000,-367618.7153185059,297.15944579679217\n", 408 | "39000,-367452.5903185059,300.89336302641715\n", 409 | "40000,-367502.4653185059,299.52073839120766\n", 410 | "41000,-367370.2153185059,295.7272258220887\n", 411 | "42000,-367363.2153185059,297.5624912019809\n", 412 | "43000,-366391.2153185059,296.6903636133109\n", 413 | "44000,-367918.2153185059,300.6013300563856\n", 414 | "45000,-368025.2153185059,298.1877675500358\n", 415 | "46000,-368510.7153185059,297.7525623829295\n", 416 | "47000,-367566.7153185059,302.13330606257665\n", 417 | "48000,-367811.7153185059,298.7717535872754\n", 418 | "49000,-366297.7153185059,298.3779695151439\n", 419 | "50000,-366514.7153185059,299.639775915897\n", 420 | "51000,-367626.8403185059,300.564672829512\n", 421 | "52000,-367110.9653185059,301.79000098686265\n", 422 | "53000,-366278.5903185059,299.02292155669943\n", 423 | "54000,-366883.5903185059,297.91922172779044\n", 424 | "55000,-368055.8403185059,299.47792155626195\n", 425 | "56000,-367863.9653185059,301.94082510984043\n", 426 | "57000,-367234.3403185059,299.1807650630395\n", 427 | "58000,-367770.8403185059,299.0379398031114\n", 428 | "59000,-367162.7153185059,299.3160943523138\n", 429 | "60000,-368148.4653185059,295.5711086449699\n", 430 | "61000,-368003.2153185059,300.57716336505075\n", 431 | "62000,-368377.7153185059,299.88767072368444\n", 432 | "63000,-367830.2153185059,298.5940528410889\n", 433 | "64000,-367928.2153185059,298.76277341236647\n", 434 | "65000,-368151.3403185059,300.07273687502686\n", 435 | "66000,-367848.5903185059,301.0169035091591\n", 436 | "67000,-366987.3403185059,299.5516404780661\n", 437 | "68000,-367460.8403185059,300.7715444776548\n", 438 | "69000,-367607.2153185059,300.6929262967641\n", 439 | "70000,-367342.9653185059,302.53248757437575\n", 440 | "71000,-367579.8403185059,300.29166336576077\n", 441 | "72000,-366964.9653185059,300.59191012787227\n", 442 | "73000,-366878.3403185059,299.43568039116207\n", 443 | "74000,-367440.4653185059,301.36041478245454\n", 444 | "75000,-367599.0903185059,301.79805296673584\n", 445 | "76000,-366959.8403185059,298.8810698438779\n", 446 | "77000,-368328.4653185059,298.03249874346585\n", 447 | "78000,-366693.2153185059,300.47231192966825\n", 448 | "79000,-366884.0903185059,300.3749681168741\n", 449 | "80000,-367117.0903185059,299.3102199054246\n", 450 | "81000,-367319.9653185059,300.44583635161155\n", 451 | "82000,-367211.8403185059,303.35869471215176\n", 452 | "83000,-367593.2153185059,301.2525033195607\n", 453 | "84000,-367114.9653185059,299.28084127822876\n", 454 | "85000,-367068.4653185059,299.8619560360876\n", 455 | "86000,-368084.7153185059,300.89443575251437\n", 456 | "87000,-368014.7153185059,299.79690636044967\n", 457 | "88000,-368173.0903185059,298.4737551391952\n", 458 | "89000,-368163.9653185059,301.768275796515\n", 459 | "90000,-366981.4653185059,297.87974120161533\n", 460 | "91000,-366375.9653185059,300.1174360686278\n", 461 | "92000,-366858.9653185059,302.94612381000496\n", 462 | "93000,-367492.7153185059,299.51912322497304\n", 463 | "94000,-367591.2153185059,298.3282521839215\n", 464 | "95000,-366832.5903185059,299.1907532869734\n", 465 | "96000,-367381.7153185059,298.54679332698635\n", 466 | "97000,-368222.4653185059,299.638998914741\n", 467 | "98000,-368710.9653185059,298.9147519912556\n", 468 | "99000,-367819.4653185059,301.5333624325752\n", 469 | "100000,-367665.7153185059,299.79090934746574\n" 470 | ] 471 | } 472 | ] 473 | } 474 | ] 475 | } 476 | -------------------------------------------------------------------------------- /charmm_gui_input_generator_based_namd_source_precompiled_CUDA_solution_md.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "nbformat": 4, 3 | "nbformat_minor": 0, 4 | "metadata": { 5 | "colab": { 6 | "name": "standard_namd_solution_md.ipynb", 7 | "provenance": [] 8 | }, 9 | "kernelspec": { 10 | "name": "python3", 11 | "display_name": "Python 3" 12 | }, 13 | "language_info": { 14 | "name": "python" 15 | }, 16 | "accelerator": "GPU" 17 | }, 18 | "cells": [ 19 | { 20 | "cell_type": "markdown", 21 | "metadata": { 22 | "id": "97iCFl061Wjt" 23 | }, 24 | "source": [ 25 | "# The default README file which is supposed to be cat into a .csh file, apparently is written in a csh format. So, let's install the csh shell environment." 26 | ] 27 | }, 28 | { 29 | "cell_type": "code", 30 | "metadata": { 31 | "colab": { 32 | "base_uri": "https://localhost:8080/" 33 | }, 34 | "id": "x8zkJcPbnJ-9", 35 | "outputId": "d6a39251-309d-4b8c-e835-4c5451786e3f" 36 | }, 37 | "source": [ 38 | "!apt-get install csh" 39 | ], 40 | "execution_count": 1, 41 | "outputs": [ 42 | { 43 | "output_type": "stream", 44 | "text": [ 45 | "Reading package lists... Done\n", 46 | "Building dependency tree \n", 47 | "Reading state information... Done\n", 48 | "The following NEW packages will be installed:\n", 49 | " csh\n", 50 | "0 upgraded, 1 newly installed, 0 to remove and 39 not upgraded.\n", 51 | "Need to get 243 kB of archives.\n", 52 | "After this operation, 358 kB of additional disk space will be used.\n", 53 | "Get:1 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 csh amd64 20110502-3ubuntu0.18.04.1 [243 kB]\n", 54 | "Fetched 243 kB in 0s (495 kB/s)\n", 55 | "Selecting previously unselected package csh.\n", 56 | "(Reading database ... 160772 files and directories currently installed.)\n", 57 | "Preparing to unpack .../csh_20110502-3ubuntu0.18.04.1_amd64.deb ...\n", 58 | "Unpacking csh (20110502-3ubuntu0.18.04.1) ...\n", 59 | "Setting up csh (20110502-3ubuntu0.18.04.1) ...\n", 60 | "update-alternatives: using /bin/bsd-csh to provide /bin/csh (csh) in auto mode\n", 61 | "Processing triggers for man-db (2.8.3-2ubuntu0.1) ...\n" 62 | ], 63 | "name": "stdout" 64 | } 65 | ] 66 | }, 67 | { 68 | "cell_type": "markdown", 69 | "metadata": { 70 | "id": "5wgZ-xIt10lq" 71 | }, 72 | "source": [ 73 | "# Now, I am gonna to upload both my input file for the namd solution simulation, and the NAMD_2021_precompiled package to the content folder. Then, we need to unzip the namd package, use the absolute path to do the simulation.\n", 74 | "Note I have previously allow notebook to get access to my google drive, and the simulation input files have been previously uploaded to my drive as well, so all I need to do here is to copy the input files and namd package to the /content/ directory" 75 | ] 76 | }, 77 | { 78 | "cell_type": "code", 79 | "metadata": { 80 | "id": "cq0cdeWH2Z7p" 81 | }, 82 | "source": [ 83 | "! tar -xvf charmm-gui_251232655.tgz" 84 | ], 85 | "execution_count": null, 86 | "outputs": [] 87 | }, 88 | { 89 | "cell_type": "code", 90 | "metadata": { 91 | "colab": { 92 | "base_uri": "https://localhost:8080/" 93 | }, 94 | "id": "Sxhw8bqQ6XGq", 95 | "outputId": "7a3ae412-6ae2-4cbb-ecd6-c97c1557611a" 96 | }, 97 | "source": [ 98 | "! wget https://www.ks.uiuc.edu/Research/namd/cvs/download/741376/NAMD_Git-2021-07-01_Linux-x86_64-multicore-CUDA.tar.gz" 99 | ], 100 | "execution_count": 6, 101 | "outputs": [ 102 | { 103 | "output_type": "stream", 104 | "text": [ 105 | "--2021-07-02 07:09:44-- https://www.ks.uiuc.edu/Research/namd/cvs/download/741376/NAMD_Git-2021-07-01_Linux-x86_64-multicore-CUDA.tar.gz\n", 106 | "Resolving www.ks.uiuc.edu (www.ks.uiuc.edu)... 130.126.120.43\n", 107 | "Connecting to www.ks.uiuc.edu (www.ks.uiuc.edu)|130.126.120.43|:443... connected.\n", 108 | "HTTP request sent, awaiting response... 200 OK\n", 109 | "Length: 169959990 (162M) [application/x-gzip]\n", 110 | "Saving to: ‘NAMD_Git-2021-07-01_Linux-x86_64-multicore-CUDA.tar.gz’\n", 111 | "\n", 112 | "NAMD_Git-2021-07-01 100%[===================>] 162.09M 99.3MB/s in 1.6s \n", 113 | "\n", 114 | "2021-07-02 07:09:48 (99.3 MB/s) - ‘NAMD_Git-2021-07-01_Linux-x86_64-multicore-CUDA.tar.gz’ saved [169959990/169959990]\n", 115 | "\n" 116 | ], 117 | "name": "stdout" 118 | } 119 | ] 120 | }, 121 | { 122 | "cell_type": "code", 123 | "metadata": { 124 | "id": "znoXSb4c7iiV" 125 | }, 126 | "source": [ 127 | "!tar -xvf NAMD_Git-2021-07-01_Linux-x86_64-multicore-CUDA.tar.gz" 128 | ], 129 | "execution_count": null, 130 | "outputs": [] 131 | }, 132 | { 133 | "cell_type": "markdown", 134 | "metadata": { 135 | "id": "UTYgvb3a8agi" 136 | }, 137 | "source": [ 138 | "# Now we need to have a look at the README file , and modify it into a csh shell file, you could just use cat command line \"cat README > run.csh\" and then use the command \" csh run.csh\" to run this script" 139 | ] 140 | }, 141 | { 142 | "cell_type": "code", 143 | "metadata": { 144 | "id": "1phgGPnZERjs" 145 | }, 146 | "source": [ 147 | "!cp /content/drive/MyDrive/2021-07-02/charmm-gui_251232655.tgz /content/" 148 | ], 149 | "execution_count": 10, 150 | "outputs": [] 151 | }, 152 | { 153 | "cell_type": "code", 154 | "metadata": { 155 | "id": "q_L6VsAIEg4B" 156 | }, 157 | "source": [ 158 | "!tar -xvf charmm-gui_251232655.tgz" 159 | ], 160 | "execution_count": null, 161 | "outputs": [] 162 | }, 163 | { 164 | "cell_type": "code", 165 | "metadata": { 166 | "id": "VEoqdXZT8Kwo" 167 | }, 168 | "source": [ 169 | "%cd /content/charmm-gui-251232655/namd/" 170 | ], 171 | "execution_count": null, 172 | "outputs": [] 173 | }, 174 | { 175 | "cell_type": "code", 176 | "metadata": { 177 | "id": "sk9WWkzP8Ky3" 178 | }, 179 | "source": [ 180 | "!cat README > run.csh " 181 | ], 182 | "execution_count": 13, 183 | "outputs": [] 184 | }, 185 | { 186 | "cell_type": "markdown", 187 | "metadata": { 188 | "id": "KoQlaigvAEFa" 189 | }, 190 | "source": [ 191 | "# To narrow the time scale I mannually opened the run.csh file and change the time from 10ns to 2ns. You also need to modify the original namd2 path to /content/NAMD_Git-2021-07-01_Linux-x86_64-multicore-CUDA/namd2." 192 | ] 193 | }, 194 | { 195 | "cell_type": "code", 196 | "metadata": { 197 | "id": "YYwjtSj8Hih1" 198 | }, 199 | "source": [ 200 | "!csh run.csh" 201 | ], 202 | "execution_count": null, 203 | "outputs": [] 204 | }, 205 | { 206 | "cell_type": "code", 207 | "metadata": { 208 | "id": "-YZ1G569IL1o" 209 | }, 210 | "source": [ 211 | "" 212 | ], 213 | "execution_count": null, 214 | "outputs": [] 215 | }, 216 | { 217 | "cell_type": "markdown", 218 | "metadata": { 219 | "id": "3TpST3TtG0B4" 220 | }, 221 | "source": [ 222 | "# One of the biggest headace of using cloud computing is that you always at a risk of losing everything at any time, after the simulation, you definately want to save the output files preperly to downloaded to local computer or like use the next code to save it to your online drive." 223 | ] 224 | }, 225 | { 226 | "cell_type": "code", 227 | "metadata": { 228 | "id": "vwq9bb6iFsKX" 229 | }, 230 | "source": [ 231 | "# Import PyDrive and associated libraries.\n", 232 | "# This only needs to be done once in a notebook.\n", 233 | "from pydrive.auth import GoogleAuth\n", 234 | "from pydrive.drive import GoogleDrive\n", 235 | "from google.colab import auth\n", 236 | "from oauth2client.client import GoogleCredentials\n", 237 | "\n", 238 | "# Authenticate and create the PyDrive client.\n", 239 | "# This only needs to be done once in a notebook.\n", 240 | "auth.authenticate_user()\n", 241 | "gauth = GoogleAuth()\n", 242 | "gauth.credentials = GoogleCredentials.get_application_default()\n", 243 | "drive = GoogleDrive(gauth)\n", 244 | "\n", 245 | "# Create & upload a text file.\n", 246 | "uploaded = drive.CreateFile({'title': 'Sample file.txt'})\n", 247 | "uploaded.SetContentString('Sample upload file content')\n", 248 | "uploaded.Upload()\n", 249 | "print('Uploaded file with ID {}'.format(uploaded.get('id')))" 250 | ], 251 | "execution_count": null, 252 | "outputs": [] 253 | }, 254 | { 255 | "cell_type": "code", 256 | "metadata": { 257 | "id": "ZwRiqDaSBXsH" 258 | }, 259 | "source": [ 260 | "" 261 | ], 262 | "execution_count": null, 263 | "outputs": [] 264 | }, 265 | { 266 | "cell_type": "code", 267 | "metadata": { 268 | "id": "3YWHETysBXuX" 269 | }, 270 | "source": [ 271 | "" 272 | ], 273 | "execution_count": null, 274 | "outputs": [] 275 | } 276 | ] 277 | } -------------------------------------------------------------------------------- /conda+rdkit+obabel.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "nbformat": 4, 3 | "nbformat_minor": 0, 4 | "metadata": { 5 | "colab": { 6 | "name": "CDD-ML-Part-2-Exploratory-Data-Analysis-Acetylcholinesterase.ipynb", 7 | "provenance": [], 8 | "collapsed_sections": [] 9 | }, 10 | "kernelspec": { 11 | "name": "python3", 12 | "display_name": "Python 3" 13 | } 14 | }, 15 | "cells": [ 16 | { 17 | "cell_type": "markdown", 18 | "metadata": { 19 | "id": "o-4IOizard4P" 20 | }, 21 | "source": [ 22 | "## **Install conda and rdkit and open babel**" 23 | ] 24 | }, 25 | { 26 | "cell_type": "code", 27 | "metadata": { 28 | "id": "H0mjQ2PcrSe5" 29 | }, 30 | "source": [ 31 | "! wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh\n", 32 | "! chmod +x Miniconda3-py37_4.8.2-Linux-x86_64.sh\n", 33 | "! bash ./Miniconda3-py37_4.8.2-Linux-x86_64.sh -b -f -p /usr/local\n", 34 | "! conda install -c rdkit rdkit -y\n", 35 | "import sys\n", 36 | "sys.path.append('/usr/local/lib/python3.7/site-packages/')" 37 | ], 38 | "execution_count": null, 39 | "outputs": [] 40 | }, 41 | { 42 | "cell_type": "code", 43 | "metadata": { 44 | "id": "xJSrclcRIX8K" 45 | }, 46 | "source": [ 47 | "!time conda install -q -y -c openbabel openbabel" 48 | ], 49 | "execution_count": null, 50 | "outputs": [] 51 | }, 52 | { 53 | "cell_type": "code", 54 | "metadata": { 55 | "id": "zl2iMbzYIhaK" 56 | }, 57 | "source": [ 58 | "import sys\n", 59 | "sys.path.append('/usr/local/lib/python3.7/site-packages/')" 60 | ], 61 | "execution_count": 3, 62 | "outputs": [] 63 | }, 64 | { 65 | "cell_type": "markdown", 66 | "metadata": { 67 | "id": "Ket71NqnclT5" 68 | }, 69 | "source": [ 70 | "Single smile conversion" 71 | ] 72 | }, 73 | { 74 | "cell_type": "code", 75 | "metadata": { 76 | "id": "uI1O58IWInH7", 77 | "colab": { 78 | "base_uri": "https://localhost:8080/" 79 | }, 80 | "outputId": "aa37eb67-1a63-48eb-c2ce-8669cfb57310" 81 | }, 82 | "source": [ 83 | "!obabel -:\"O=C1N=C(N2CCN(C(C=C)=O)C[C@@H]2C)C3=CC(F)=C(C4=C(O)C=CC=C4F)N=C3[N@@]1[C@@]5=C(C)C=CN=C5C(C)C\" -osdf -O AMG510.sdf --gen3d" 84 | ], 85 | "execution_count": 13, 86 | "outputs": [ 87 | { 88 | "output_type": "stream", 89 | "text": [ 90 | "==============================\n", 91 | "*** Open Babel Warning in ParseSmiles\n", 92 | " Ignoring stereochemistry. Not enough connections to this atom. \n", 93 | "==============================\n", 94 | "*** Open Babel Warning in ParseSmiles\n", 95 | " Ignoring stereochemistry. Not enough connections to this atom. \n", 96 | "1 molecule converted\n" 97 | ], 98 | "name": "stdout" 99 | } 100 | ] 101 | }, 102 | { 103 | "cell_type": "markdown", 104 | "metadata": { 105 | "id": "yMoS9cbMcuxG" 106 | }, 107 | "source": [ 108 | "Batch smiles conversion. There are two lines of smiles inside \"example.smi\"." 109 | ] 110 | }, 111 | { 112 | "cell_type": "code", 113 | "metadata": { 114 | "id": "FTuuKDuIbhj7" 115 | }, 116 | "source": [ 117 | "!echo \"O=C1N=C(N2CCN(C(C=C)=O)C[C@@H]2C)C3=CC(F)=C(C4=C(O)C=CC=C4F)N=C3[N@@]1[C@@]5=C(C)C=CN=C5C(C)C\" > example.smi" 118 | ], 119 | "execution_count": 10, 120 | "outputs": [] 121 | }, 122 | { 123 | "cell_type": "code", 124 | "metadata": { 125 | "id": "DsgVSffSbtB-" 126 | }, 127 | "source": [ 128 | "!echo \"O=C1N=C(N2CCN(C(C=C)=O)C[C@@H]2C)C3=CC(F)=C(C4=C(O)C=CC=C4F)N=C3[N@@]1[C@@]5=C(C)C=CN=C5C(C)C\" >> example.smi" 129 | ], 130 | "execution_count": 11, 131 | "outputs": [] 132 | }, 133 | { 134 | "cell_type": "code", 135 | "metadata": { 136 | "id": "ePl7fWwiZt3Y", 137 | "outputId": "77fb17e1-a82b-4e56-8af7-312b4c06239c", 138 | "colab": { 139 | "base_uri": "https://localhost:8080/" 140 | } 141 | }, 142 | "source": [ 143 | "!obabel example.smi -O example.sdf --gen3d" 144 | ], 145 | "execution_count": 14, 146 | "outputs": [ 147 | { 148 | "output_type": "stream", 149 | "text": [ 150 | "==============================\n", 151 | "*** Open Babel Warning in ParseSmiles\n", 152 | " Ignoring stereochemistry. Not enough connections to this atom. \n", 153 | "==============================\n", 154 | "*** Open Babel Warning in ParseSmiles\n", 155 | " Ignoring stereochemistry. Not enough connections to this atom. \n", 156 | "==============================\n", 157 | "*** Open Babel Warning in ParseSmiles\n", 158 | " Ignoring stereochemistry. Not enough connections to this atom. \n", 159 | "==============================\n", 160 | "*** Open Babel Warning in ParseSmiles\n", 161 | " Ignoring stereochemistry. Not enough connections to this atom. \n", 162 | "2 molecules converted\n" 163 | ], 164 | "name": "stdout" 165 | } 166 | ] 167 | } 168 | ] 169 | } -------------------------------------------------------------------------------- /conda-rdkit-smiles-fragmentation-recap.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "nbformat": 4, 3 | "nbformat_minor": 0, 4 | "metadata": { 5 | "colab": { 6 | "name": "“CDD-ML-Part-2-Exploratory-Data-Analysis-Acetylcholinesterase.ipynb”的副本", 7 | "provenance": [], 8 | "collapsed_sections": [], 9 | "include_colab_link": true 10 | }, 11 | "kernelspec": { 12 | "name": "python3", 13 | "display_name": "Python 3" 14 | } 15 | }, 16 | "cells": [ 17 | { 18 | "cell_type": "markdown", 19 | "metadata": { 20 | "id": "view-in-github", 21 | "colab_type": "text" 22 | }, 23 | "source": [ 24 | "\"Open" 25 | ] 26 | }, 27 | { 28 | "cell_type": "markdown", 29 | "metadata": { 30 | "id": "o-4IOizard4P" 31 | }, 32 | "source": [ 33 | "## **Install conda and rdkit and fragment a molecule**\n", 34 | "\n", 35 | "---\n", 36 | "\n" 37 | ] 38 | }, 39 | { 40 | "cell_type": "code", 41 | "metadata": { 42 | "id": "H0mjQ2PcrSe5" 43 | }, 44 | "source": [ 45 | "! wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh\n", 46 | "! chmod +x Miniconda3-py37_4.8.2-Linux-x86_64.sh\n", 47 | "! bash ./Miniconda3-py37_4.8.2-Linux-x86_64.sh -b -f -p /usr/local\n", 48 | "! conda install -c rdkit rdkit -y\n", 49 | "import sys\n", 50 | "sys.path.append('/usr/local/lib/python3.7/site-packages/')" 51 | ], 52 | "execution_count": null, 53 | "outputs": [] 54 | }, 55 | { 56 | "cell_type": "code", 57 | "metadata": { 58 | "id": "ouBs_PpRjOzq", 59 | "colab": { 60 | "base_uri": "https://localhost:8080/" 61 | }, 62 | "outputId": "82cecbfc-9bd3-49db-ff4f-946ba7fced31" 63 | }, 64 | "source": [ 65 | "from rdkit import Chem\n", 66 | "from rdkit.Chem import Recap\n", 67 | "m = Chem.MolFromSmiles('c1ccccc1OCCOC(=O)CC')\n", 68 | "hierarch = Recap.RecapDecompose(m)\n", 69 | "type(hierarch)" 70 | ], 71 | "execution_count": null, 72 | "outputs": [ 73 | { 74 | "output_type": "execute_result", 75 | "data": { 76 | "text/plain": [ 77 | "rdkit.Chem.Recap.RecapHierarchyNode" 78 | ] 79 | }, 80 | "metadata": { 81 | "tags": [] 82 | }, 83 | "execution_count": 2 84 | } 85 | ] 86 | }, 87 | { 88 | "cell_type": "code", 89 | "metadata": { 90 | "id": "0NOh-hsVjPB7", 91 | "colab": { 92 | "base_uri": "https://localhost:8080/", 93 | "height": 38 94 | }, 95 | "outputId": "f7ccdf13-8193-4eaf-eb52-f5d91db35ea1" 96 | }, 97 | "source": [ 98 | "hierarch.smiles" 99 | ], 100 | "execution_count": null, 101 | "outputs": [ 102 | { 103 | "output_type": "execute_result", 104 | "data": { 105 | "application/vnd.google.colaboratory.intrinsic+json": { 106 | "type": "string" 107 | }, 108 | "text/plain": [ 109 | "'CCC(=O)OCCOc1ccccc1'" 110 | ] 111 | }, 112 | "metadata": { 113 | "tags": [] 114 | }, 115 | "execution_count": 3 116 | } 117 | ] 118 | }, 119 | { 120 | "cell_type": "code", 121 | "metadata": { 122 | "id": "JK-dTMLkjPK4", 123 | "colab": { 124 | "base_uri": "https://localhost:8080/" 125 | }, 126 | "outputId": "518b6361-9410-459a-a4be-680606a5fe19" 127 | }, 128 | "source": [ 129 | "ks=hierarch.children.keys()\n", 130 | "sorted(ks)" 131 | ], 132 | "execution_count": null, 133 | "outputs": [ 134 | { 135 | "output_type": "execute_result", 136 | "data": { 137 | "text/plain": [ 138 | "['*C(=O)CC', '*CCOC(=O)CC', '*CCOc1ccccc1', '*OCCOc1ccccc1', '*c1ccccc1']" 139 | ] 140 | }, 141 | "metadata": { 142 | "tags": [] 143 | }, 144 | "execution_count": 4 145 | } 146 | ] 147 | }, 148 | { 149 | "cell_type": "code", 150 | "metadata": { 151 | "id": "I5JK-CTNjPTZ", 152 | "colab": { 153 | "base_uri": "https://localhost:8080/" 154 | }, 155 | "outputId": "462f445e-b06d-462d-ff64-fee205d48dc9" 156 | }, 157 | "source": [ 158 | "ks=hierarch.GetLeaves().keys()\n", 159 | "ks=sorted(ks)\n", 160 | "ks\n" 161 | ], 162 | "execution_count": null, 163 | "outputs": [ 164 | { 165 | "output_type": "execute_result", 166 | "data": { 167 | "text/plain": [ 168 | "['*C(=O)CC', '*CCO*', '*CCOc1ccccc1', '*c1ccccc1']" 169 | ] 170 | }, 171 | "metadata": { 172 | "tags": [] 173 | }, 174 | "execution_count": 5 175 | } 176 | ] 177 | }, 178 | { 179 | "cell_type": "code", 180 | "metadata": { 181 | "id": "Q1vQqeVJjPZt", 182 | "colab": { 183 | "base_uri": "https://localhost:8080/", 184 | "height": 38 185 | }, 186 | "outputId": "f3cfd684-903e-44a6-aafc-cb5940abf6ce" 187 | }, 188 | "source": [ 189 | "leaf = hierarch.GetLeaves()[ks[0]]\n", 190 | "Chem.MolToSmiles(leaf.mol)" 191 | ], 192 | "execution_count": null, 193 | "outputs": [ 194 | { 195 | "output_type": "execute_result", 196 | "data": { 197 | "application/vnd.google.colaboratory.intrinsic+json": { 198 | "type": "string" 199 | }, 200 | "text/plain": [ 201 | "'*C(=O)CC'" 202 | ] 203 | }, 204 | "metadata": { 205 | "tags": [] 206 | }, 207 | "execution_count": 6 208 | } 209 | ] 210 | } 211 | ] 212 | } -------------------------------------------------------------------------------- /gromacs_abf_run.sh: -------------------------------------------------------------------------------- 1 | for (( a = 0; a <=2; a++ )) 2 | do 3 | for (( b = 6; b <10; b++ )) 4 | do 5 | cd lambda.$a.$b 6 | mkdir ENMIN 7 | cd ENMIN 8 | gmx grompp -f ../../MDP/ENMIN/enmin.$a.$b.mdp -c ../../solv_ions.gro -p ../../topol.top -n ../../index_jz4.ndx -o enmin.tpr 9 | gmx mdrun -v -stepout 1000 -s enmin.tpr -deffnm enmin -nb gpu 10 | cd ../ 11 | mkdir NVT 12 | cd NVT 13 | gmx grompp -f ../../MDP/NVT/nvt.$a.$b.mdp -c ../ENMIN/enmin.gro -p ../../topol.top -n ../../index.ndx -o nvt.tpr -r ../../solv_ions.gro 14 | gmx mdrun -stepout 1000 -s nvt.tpr -deffnm nvt -nb gpu 15 | cd ../ 16 | mkdir NPT 17 | cd NPT 18 | gmx grompp -f ../../MDP/NPT/npt.$a.$b.mdp -c ../NVT/nvt.gro -t ../NVT/nvt.cpt -p ../../topol.top -n ../../index.ndx -o npt.tpr -r ../../solv_ions.gro 19 | gmx mdrun -stepout 1000 -s npt.tpr -deffnm npt -nb gpu 20 | cd ../ 21 | mkdir PROD 22 | cd PROD 23 | gmx grompp -f ../../MDP/PROD/prod.$a.$b.mdp -c ../NPT/npt.gro -t ../NPT/npt.cpt -p ../../topol.top -n ../../index.ndx -o prod.tpr 24 | gmx mdrun -stepout 1000 -s prod.tpr -deffnm prod -dhdl dhdl -nb gpu 25 | 26 | cd ../../ 27 | done 28 | done 29 | -------------------------------------------------------------------------------- /ipymol.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "(example from http://pymolwiki.org/index.php/Gallery )" 8 | ] 9 | }, 10 | { 11 | "cell_type": "code", 12 | "execution_count": 1, 13 | "metadata": {}, 14 | "outputs": [ 15 | { 16 | "name": "stdout", 17 | "output_type": "stream", 18 | "text": [ 19 | "Populating the interactive namespace from numpy and matplotlib\n" 20 | ] 21 | } 22 | ], 23 | "source": [ 24 | "%pylab inline\n", 25 | "from ipymol import viewer as pymol" 26 | ] 27 | }, 28 | { 29 | "cell_type": "code", 30 | "execution_count": 2, 31 | "metadata": {}, 32 | "outputs": [], 33 | "source": [ 34 | "pymol.start()" 35 | ] 36 | }, 37 | { 38 | "cell_type": "code", 39 | "execution_count": 4, 40 | "metadata": {}, 41 | "outputs": [], 42 | "source": [ 43 | "pymol.do('fetch 3uex, struct, async=0;')\n", 44 | "pymol.do('remove solvent; ')\n", 45 | "\n", 46 | "# smoothing parameters\n", 47 | "pymol.do('alter all, b=10; alter all, q=1; set gaussian_resolution, 7.6;')\n", 48 | "pymol.do('map_new map, gaussian, 1, n. C+O+N+CA, 5; isosurface surf, map, 1.5;')\n", 49 | "\n", 50 | "# color struct according to atom count\n", 51 | "pymol.do('spectrum count, rainbow, struct')\n", 52 | "\n", 53 | "# color the map based on the b-factors of the underlying protein\n", 54 | "pymol.do('cmd.ramp_new(\"ramp\", \"struct\", [0,10,10], \"rainbow\") ')\n", 55 | " \n", 56 | "# set the surface color\n", 57 | "pymol.do('cmd.set(\"surface_color\", \"ramp\", \"surf\")')\n", 58 | " \n", 59 | "# hide the ramp and lines\n", 60 | "pymol.do('disable ramp; hide lines;')\n", 61 | "\n", 62 | "pymol.do('show sticks, org; show spheres, org;')\n", 63 | "\n", 64 | "pymol.do('color magenta, org')\n", 65 | "pymol.do('set_bond stick_radius, 0.13, org; set sphere_scale, 0.26, org;')\n", 66 | " \n", 67 | "pymol.do('set_bond stick_radius, 0.13, org; set_bond stick_color, white, org; set sphere_scale, 0.26, org;')\n", 68 | "\n", 69 | "pymol.do('set_view (\\\n", 70 | " -0.877680123, 0.456324875, -0.146428943,\\\n", 71 | " 0.149618521, -0.029365506, -0.988305628,\\\n", 72 | " -0.455291569, -0.889327347, -0.042500813,\\\n", 73 | " -0.000035629, 0.000030629, -37.112102509,\\\n", 74 | " -3.300258160, 6.586110592, 22.637466431,\\\n", 75 | " 8.231912613, 65.999290466, -50.000000000 );')\n", 76 | "\n", 77 | "pymol.do('ray;')\n", 78 | "\n", 79 | "pymol.show()\n", 80 | "pymol.do('png png0.png;')" 81 | ] 82 | }, 83 | { 84 | "cell_type": "code", 85 | "execution_count": null, 86 | "metadata": {}, 87 | "outputs": [], 88 | "source": [] 89 | } 90 | ], 91 | "metadata": { 92 | "kernelspec": { 93 | "display_name": "Python 3", 94 | "language": "python", 95 | "name": "python3" 96 | }, 97 | "language_info": { 98 | "codemirror_mode": { 99 | "name": "ipython", 100 | "version": 3 101 | }, 102 | "file_extension": ".py", 103 | "mimetype": "text/x-python", 104 | "name": "python", 105 | "nbconvert_exporter": "python", 106 | "pygments_lexer": "ipython3", 107 | "version": "3.8.5" 108 | } 109 | }, 110 | "nbformat": 4, 111 | "nbformat_minor": 4 112 | } 113 | -------------------------------------------------------------------------------- /namd2.14-cuda-GPU-charmm-gui-with-Colab.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "nbformat": 4, 3 | "nbformat_minor": 0, 4 | "metadata": { 5 | "colab": { 6 | "name": "namd.ipynb", 7 | "provenance": [], 8 | "collapsed_sections": [] 9 | }, 10 | "kernelspec": { 11 | "name": "python3", 12 | "display_name": "Python 3" 13 | }, 14 | "accelerator": "GPU" 15 | }, 16 | "cells": [ 17 | { 18 | "cell_type": "markdown", 19 | "metadata": { 20 | "id": "_AVJH7JDvLtK" 21 | }, 22 | "source": [ 23 | "# This is a guideline of a standard solution NAMD simulation, based on input files returned from Charmm GUI solution input generator.\n", 24 | "Created by quantaosun@gmail.com;\n", 25 | "**Github: quantaosun/notebook**\n" 26 | ] 27 | }, 28 | { 29 | "cell_type": "markdown", 30 | "metadata": { 31 | "id": "ULnaC54rwHDS" 32 | }, 33 | "source": [ 34 | "下载支持GPU加速的NAMD的免安装版本NAMD2.14-cuda. 或者最新版的nightly build 版本的CUDA预先编译版本的。" 35 | ] 36 | }, 37 | { 38 | "cell_type": "code", 39 | "metadata": { 40 | "id": "HS81BcMQncVW" 41 | }, 42 | "source": [ 43 | "# Download the NAMD binary\n", 44 | "!wget https://www.ks.uiuc.edu/Research/namd/2.14/download/946183/NAMD_2.14_Linux-x86_64-multicore-CUDA.tar.gz" 45 | ], 46 | "execution_count": null, 47 | "outputs": [] 48 | }, 49 | { 50 | "cell_type": "code", 51 | "metadata": { 52 | "id": "wb0AxjOAm68j" 53 | }, 54 | "source": [ 55 | "# Extract the file\n", 56 | "# !tar -zxf /content/NAMD_2.14_Linux-x86_64-multicore-CUDA.tar.gz\n", 57 | "!tar -zxf NAMD_2.14_Linux-x86_64-multicore-CUDA.tar.gz" 58 | ], 59 | "execution_count": null, 60 | "outputs": [] 61 | }, 62 | { 63 | "cell_type": "markdown", 64 | "metadata": { 65 | "id": "qyLXerWTnD8o" 66 | }, 67 | "source": [ 68 | "**Please make sure to upload your CHARMM GUI package and extract it.\n", 69 | "，我默认你已经前往Charmm GUI 网页自行通过input generator> solutino builder 生成了下面模拟所需的输入文件，你需要上传到这里** " 70 | ] 71 | }, 72 | { 73 | "cell_type": "code", 74 | "metadata": { 75 | "id": "rH7dYekynAIf" 76 | }, 77 | "source": [ 78 | "!tar -zxf charmm-gui-solution.tgz\n" 79 | ], 80 | "execution_count": null, 81 | "outputs": [] 82 | }, 83 | { 84 | "cell_type": "code", 85 | "metadata": { 86 | "id": "XSsozm-8rHiO" 87 | }, 88 | "source": [ 89 | "!pwd\n", 90 | "!mkdir namd_result\n", 91 | "%cd namd_result/" 92 | ], 93 | "execution_count": null, 94 | "outputs": [] 95 | }, 96 | { 97 | "cell_type": "markdown", 98 | "metadata": { 99 | "id": "o3yGatZOsU8Z" 100 | }, 101 | "source": [ 102 | "**Before you move any further, please switch runtime to \"GPU\", 记得切换运行环境哦**" 103 | ] 104 | }, 105 | { 106 | "cell_type": "markdown", 107 | "metadata": { 108 | "id": "Pt76s4nXyDWR" 109 | }, 110 | "source": [ 111 | "**假设我们只想快速的完成1ns的模拟** In case you just want a quick 1ns simulation" 112 | ] 113 | }, 114 | { 115 | "cell_type": "markdown", 116 | "metadata": { 117 | "id": "xADSKYRxwctz" 118 | }, 119 | "source": [ 120 | "假设我们只想快速的完成1ns 的模拟，以下具体的namd 和文件路径，以你自己的为准，请适当修改。我们从第四步开始继续模拟，我们默认charmm gui 已经为我们完成了第三步" 121 | ] 122 | }, 123 | { 124 | "cell_type": "code", 125 | "metadata": { 126 | "id": "dUZd7W5FO167" 127 | }, 128 | "source": [ 129 | "# run NAMD. You should change the paths to correspond to the files\n", 130 | "!/content/NAMD_2.14_Linux-x86_64-multicore-CUDA/namd2 +p4 /content/charmm-gui-0456126325/namd/step4_equilibration.inp > step4.log" 131 | ], 132 | "execution_count": null, 133 | "outputs": [] 134 | }, 135 | { 136 | "cell_type": "code", 137 | "metadata": { 138 | "id": "gNCBi827rm9H" 139 | }, 140 | "source": [ 141 | "# run NAMD. You should change the paths to correspond to the files\n", 142 | "!/content/NAMD_2.14_Linux-x86_64-multicore-CUDA/namd2 +p4 /content/charmm-gui-0456126325/namd/step5_production.inp > step5.log" 143 | ], 144 | "execution_count": null, 145 | "outputs": [] 146 | }, 147 | { 148 | "cell_type": "markdown", 149 | "metadata": { 150 | "id": "t5zP_BFuymGR" 151 | }, 152 | "source": [ 153 | "**假设我们想完成10ns 的模拟** " 154 | ] 155 | }, 156 | { 157 | "cell_type": "markdown", 158 | "metadata": { 159 | "id": "81nKP3HVyHJZ" 160 | }, 161 | "source": [ 162 | "假设我们想完成10ns 的模拟，我们需要用跟随Charmm gui 返回文件而来的， README, 其包含了需要运行10ns 的循环模拟指令，指令是以csh shell 语言的形式写的，我们只需要 cat README > run.csh 然后在colab, 运行，\"csh run.csh\"" 163 | ] 164 | }, 165 | { 166 | "cell_type": "code", 167 | "metadata": { 168 | "id": "JEQVkHgnyovo" 169 | }, 170 | "source": [ 171 | "%%bash\n", 172 | "cat README > run.csh\n", 173 | "csh run.csh" 174 | ], 175 | "execution_count": null, 176 | "outputs": [] 177 | }, 178 | { 179 | "cell_type": "markdown", 180 | "metadata": { 181 | "id": "YUEs4FBCvGMr" 182 | }, 183 | "source": [ 184 | "**Use next section if you have multiple dcd files**" 185 | ] 186 | }, 187 | { 188 | "cell_type": "markdown", 189 | "metadata": { 190 | "id": "w5ZcsbAQzepR" 191 | }, 192 | "source": [ 193 | "" 194 | ] 195 | }, 196 | { 197 | "cell_type": "code", 198 | "metadata": { 199 | "id": "qSbmuu95ryCG" 200 | }, 201 | "source": [ 202 | "# Download CatDCD to combine the dcd files into1.log\n", 203 | "#!wget https://www.ks.uiuc.edu/Development/MDTools/catdcd/files/catdcd-4.0b.tar.gz\n", 204 | "#!tar -zxf catdcd-4.0b.tar.gz" 205 | ], 206 | "execution_count": null, 207 | "outputs": [] 208 | }, 209 | { 210 | "cell_type": "code", 211 | "metadata": { 212 | "id": "P5GaS_4Xssd-" 213 | }, 214 | "source": [ 215 | "# Run CatDCD. follow the instructions\n", 216 | "#!/content/LINUX/bin/catdcd4.0/catdcd" 217 | ], 218 | "execution_count": null, 219 | "outputs": [] 220 | }, 221 | { 222 | "cell_type": "code", 223 | "metadata": { 224 | "id": "AqsIO7F6syY0" 225 | }, 226 | "source": [ 227 | "" 228 | ], 229 | "execution_count": null, 230 | "outputs": [] 231 | } 232 | ] 233 | } -------------------------------------------------------------------------------- /namd_charmm_gui_solution.csh: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | # 3 | 4 | # Generated by CHARMM-GUI (http://www.charmm-gui.org) v3.5 5 | # 6 | # The following shell script assumes your NAMD executable is namd2 and that 7 | # the NAMD inputs are located in the current directory. 8 | # 9 | # Only one processor is used below. To parallelize NAMD, use this scheme: 10 | # charmrun namd2 +p4 input_file.inp > output_file.out 11 | # where the "4" in "+p4" is replaced with the actual number of processors you 12 | # intend to use. 13 | 14 | set equi_prefix = step4_equilibration 15 | set prod_prefix = step5_production 16 | set prod_step = step5 17 | 18 | # Running equilibration step 19 | namd2 ${equi_prefix}.inp > ${equi_prefix}.out 20 | 21 | # Running production for 10 nanoseconds 22 | set cnt = 1 23 | set cntmax = 10 24 | 25 | while ( ${cnt} <= ${cntmax} ) 26 | # create appropriate input file using ${prod_prefix}.inp as template 27 | if ( ${cnt} == 1 ) then 28 | set outputname = "${prod_step}_${cnt}" 29 | # change only the output name 30 | sed "s/${prod_prefix}/${outputname}/" ${prod_prefix}.inp > ${prod_step}_run.inp 31 | else 32 | @ cntprev = ${cnt} - 1 33 | set inputname = "${prod_step}_${cntprev}" 34 | set outputname = "${prod_step}_${cnt}" 35 | # change input and output names from template file 36 | sed "s/${equi_prefix}/${inputname}/" ${prod_prefix}.inp | \ 37 | sed "s/${prod_prefix}/${outputname}/" > ${prod_step}_run.inp 38 | endif 39 | 40 | # run the simulation for 1 nanosecond 41 | namd2 ${prod_step}_run.inp > ${outputname}.out 42 | 43 | @ cnt += 1 44 | end 45 | 46 | 47 | -------------------------------------------------------------------------------- /namd_charmm_gui_solution.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #1.Generate 10 conf files for 10 ns simulation 3 | for (( a=1; a<=10; a++ )) 4 | do 5 | cat step5_production.inp > step5_production.$a.inp 6 | done 7 | #2.In the 1st loop, we will only substitute the output name from "step5_production" to "step5_production.$a", that's all 8 | for (( a=1; a<=10; a++ )); 9 | do sed -i "s/step5_production/step5_production.$a/" step5_production.$a.inp; 10 | done 11 | #3.In this for loop we gonna to replace the input file name from "step4equlibration" to "step5_production.$($a-1)" from 2 to 10, while keep the 1st step5_production.1.inp untouched. 12 | for (( a=2; a<=10; a++ )) 13 | do sed -i "s/step4_equilibration/step5_production.$[a-1]/" step5_production.$a.inp 14 | done 15 | #4.Finally, we could run on AI Studio, in a bash style, not as a csh style. 16 | #with namd2 (modify the+p4 option with your actual CPU numbers) run command inserted inside the loop, something like below: 17 | 18 | #5.Equilibration 19 | /home/aistudio/NAMD_Git-2021-05-17_Linux-x86_64-multicore-CUDA/namd2 step4_equilibration.inp > step4_equilibration.out2 && 20 | #6.Production 21 | for (( a=1; a <=10; a++ )) 22 | do 23 | /home/aistudio/NAMD_Git-2021-05-17_Linux-x86_64-multicore-CUDA/namd2 +p4 step5_production.$a.inp > step5_production.$a.out3 24 | done 25 | -------------------------------------------------------------------------------- /绝对结合自由能平衡+_eABF_二合一BFEE_1mq5_equlibratioin.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "nbformat": 4, 3 | "nbformat_minor": 0, 4 | "metadata": { 5 | "accelerator": "GPU", 6 | "colab": { 7 | "name": "绝对结合自由能平衡+ eABF 二合一BFEE_1mq5_equlibratioin", 8 | "provenance": [], 9 | "collapsed_sections": [] 10 | }, 11 | "kernelspec": { 12 | "display_name": "Python 3", 13 | "name": "python3" 14 | }, 15 | "language_info": { 16 | "name": "python" 17 | } 18 | }, 19 | "cells": [ 20 | { 21 | "cell_type": "markdown", 22 | "metadata": { 23 | "id": "m104f3yfpS21" 24 | }, 25 | "source": [ 26 | "👌🏻👌👌👌**切换到GPU模式** SWITCH to GPU" 27 | ] 28 | }, 29 | { 30 | "cell_type": "markdown", 31 | "metadata": { 32 | "id": "k_8NFqafKBAJ" 33 | }, 34 | "source": [ 35 | "**This is a mixture script of an equilbration MD and a follow up free energy bidning estimator run. You could use some of the cells to first finish a normal solution simulation from the input generated from Charmm GUI; then use VMD BFEE module to generate input files needed for the eABF run, then use the other cells to perform 8 simulation regarding to different collective variables, and at last generated the dG number we want ultimately with VMD BFEE again.**" 36 | ] 37 | }, 38 | { 39 | "cell_type": "markdown", 40 | "metadata": { 41 | "id": "fjVs97nYHrY3" 42 | }, 43 | "source": [ 44 | "**因目前2021-09的CGff无法正确处理F Cl Br 的孤对电子；在使用charmm gui时注意选择open MM 作为小分子的立场选项。**" 45 | ] 46 | }, 47 | { 48 | "cell_type": "code", 49 | "metadata": { 50 | "id": "0MHrrdgqHpNP" 51 | }, 52 | "source": [ 53 | "!apt-get install vim" 54 | ], 55 | "execution_count": null, 56 | "outputs": [] 57 | }, 58 | { 59 | "cell_type": "code", 60 | "metadata": { 61 | "colab": { 62 | "base_uri": "https://localhost:8080/" 63 | }, 64 | "id": "ViDk3GnnnkA3", 65 | "outputId": "3d7aa6c9-d682-4d01-ca18-6a2f6bb9b03e" 66 | }, 67 | "source": [ 68 | "!sudo apt-get install csh" 69 | ], 70 | "execution_count": 1, 71 | "outputs": [ 72 | { 73 | "output_type": "stream", 74 | "name": "stdout", 75 | "text": [ 76 | "Reading package lists... Done\n", 77 | "Building dependency tree \n", 78 | "Reading state information... Done\n", 79 | "The following NEW packages will be installed:\n", 80 | " csh\n", 81 | "0 upgraded, 1 newly installed, 0 to remove and 37 not upgraded.\n", 82 | "Need to get 243 kB of archives.\n", 83 | "After this operation, 358 kB of additional disk space will be used.\n", 84 | "Get:1 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 csh amd64 20110502-3ubuntu0.18.04.1 [243 kB]\n", 85 | "Fetched 243 kB in 1s (241 kB/s)\n", 86 | "debconf: unable to initialize frontend: Dialog\n", 87 | "debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76, <> line 1.)\n", 88 | "debconf: falling back to frontend: Readline\n", 89 | "debconf: unable to initialize frontend: Readline\n", 90 | "debconf: (This frontend requires a controlling tty.)\n", 91 | "debconf: falling back to frontend: Teletype\n", 92 | "dpkg-preconfigure: unable to re-open stdin: \n", 93 | "Selecting previously unselected package csh.\n", 94 | "(Reading database ... 155013 files and directories currently installed.)\n", 95 | "Preparing to unpack .../csh_20110502-3ubuntu0.18.04.1_amd64.deb ...\n", 96 | "Unpacking csh (20110502-3ubuntu0.18.04.1) ...\n", 97 | "Setting up csh (20110502-3ubuntu0.18.04.1) ...\n", 98 | "update-alternatives: using /bin/bsd-csh to provide /bin/csh (csh) in auto mode\n", 99 | "Processing triggers for man-db (2.8.3-2ubuntu0.1) ...\n" 100 | ] 101 | } 102 | ] 103 | }, 104 | { 105 | "cell_type": "code", 106 | "metadata": { 107 | "id": "OUo2VW3-bZ5Y" 108 | }, 109 | "source": [ 110 | "! cp /content/drive/MyDrive/Colab谷歌计算平台50美元算力测试/NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA-SingleNode.tar.gz ./" 111 | ], 112 | "execution_count": 2, 113 | "outputs": [] 114 | }, 115 | { 116 | "cell_type": "code", 117 | "metadata": { 118 | "id": "UwjRTga7plX-" 119 | }, 120 | "source": [ 121 | "#!cp /content/drive/MyDrive/Colab谷歌计算平台50美元算力测试/1mq5_charmm-gui_31.tgz ./" 122 | ], 123 | "execution_count": null, 124 | "outputs": [] 125 | }, 126 | { 127 | "cell_type": "code", 128 | "metadata": { 129 | "id": "iOpsOd4ZEFBk" 130 | }, 131 | "source": [ 132 | "#!cp /content/drive/MyDrive/Colab谷歌计算平台50美元算力测试/1mq5_eABF.tar.gz ./" 133 | ], 134 | "execution_count": null, 135 | "outputs": [] 136 | }, 137 | { 138 | "cell_type": "code", 139 | "metadata": { 140 | "id": "VSyYMgGNCI2L" 141 | }, 142 | "source": [ 143 | "!cp /content/drive/MyDrive/Colab谷歌计算平台50美元算力测试/charmm-gui-openMM.tgz ./" 144 | ], 145 | "execution_count": 3, 146 | "outputs": [] 147 | }, 148 | { 149 | "cell_type": "code", 150 | "metadata": { 151 | "colab": { 152 | "base_uri": "https://localhost:8080/" 153 | }, 154 | "id": "1depg10hc67R", 155 | "outputId": "0889f2aa-0eda-4560-92d8-29833cdd43af" 156 | }, 157 | "source": [ 158 | "!tar -xvf NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA-SingleNode.tar.gz" 159 | ], 160 | "execution_count": 4, 161 | "outputs": [ 162 | { 163 | "output_type": "stream", 164 | "name": "stdout", 165 | "text": [ 166 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/\n", 167 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/charmd\n", 168 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/charmrun\n", 169 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/license.txt\n", 170 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/flipdcd\n", 171 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/sortreplicas\n", 172 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/README.txt\n", 173 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/announce.txt\n", 174 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/charmd_faceless\n", 175 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/psfgen\n", 176 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/namd3\n", 177 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/\n", 178 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf_integrate/\n", 179 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf_integrate/abf_data.h\n", 180 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf_integrate/abf_data.cpp\n", 181 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf_integrate/abf_integrate.cpp\n", 182 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf_integrate/Makefile\n", 183 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/\n", 184 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/toppar/\n", 185 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/toppar/conf_cph36_cgenff.json\n", 186 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/toppar/conf_cph36_prot.json\n", 187 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/toppar/top_cph36_cgenff.rtf\n", 188 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/toppar/par_cph36_prot.prm\n", 189 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/toppar/toppar_water_ions.str\n", 190 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/toppar/par_cph36_cgenff.prm\n", 191 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/toppar/top_cph36_prot.rtf\n", 192 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/toppar/par_all36_prot.prm\n", 193 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/\n", 194 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/ace/\n", 195 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/ace/ace.namd\n", 196 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/ace/topology/\n", 197 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/ace/topology/ace.pdb\n", 198 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/ace/topology/ace.psf\n", 199 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/ace/topology/ace.xsc\n", 200 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/ace/ace_restart.namd\n", 201 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/bbl/\n", 202 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/bbl/topology/\n", 203 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/bbl/topology/bbl.psf\n", 204 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/bbl/topology/bbl.pdb\n", 205 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/bbl/topology/bbl.xsc\n", 206 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/examples/bbl/bbl.namd\n", 207 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/namdcph.tcl\n", 208 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/namdcph/\n", 209 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/namdcph/json.tcl\n", 210 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/namdcph/cphphsampler.tcl\n", 211 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/namdcph/cphpsfgen.tcl\n", 212 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/namdcph/namdcph/namdtcl.tcl\n", 213 | 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"NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/example/load_all.vmd\n", 336 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/example/alanin.psf\n", 337 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/example/job1.conf\n", 338 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/example/mplexjob0.conf\n", 339 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/example/alanin_base.namd\n", 340 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/example/job0.conf\n", 341 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/example/mplexjob1.conf\n", 342 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/example/alanin.params\n", 343 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/example/fold_alanin.conf\n", 344 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/make_output_dirs.sh\n", 345 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/\n", 346 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/par_all36_prot_tip3.prm\n", 347 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/aaqaa3_rest2_test.namd\n", 348 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/aaqaa3_solvate.pdb\n", 349 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/aaqaa3_1_xplor.psf\n", 350 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/README\n", 351 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/aaqaa3.spt\n", 352 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/aaqaa3_rest2_base.namd\n", 353 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/restart_1.conf\n", 354 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/equinpt.xsc\n", 355 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/rest2_remd.namd\n", 356 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/equinpt.coor\n", 357 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/replica/REST2/init.conf\n", 358 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/\n", 359 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/scripts/\n", 360 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/scripts/testRand.tcl\n", 361 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/scripts/ramd-5.tcl\n", 362 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/scripts/ramd-5_script.tcl\n", 363 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/scripts/README\n", 364 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/scripts/testRand.dat\n", 365 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/examples/\n", 366 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/examples/1WDHI/\n", 367 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/examples/1WDHI/RAMD-force.sh\n", 368 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/examples/DCL/\n", 369 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/examples/DCL/RAMD-force.sh\n", 370 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/examples/DCL/README.examples\n", 371 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/examples/README\n", 372 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-5/README\n", 373 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/\n", 374 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/scripts/\n", 375 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/scripts/ramd-4.1_script.tcl\n", 376 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/scripts/ramd-4.1.tcl\n", 377 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/scripts/vectors.tcl\n", 378 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/examples/\n", 379 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/examples/README.examples\n", 380 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/examples/example_ramd-md_output/\n", 381 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/examples/example_ramd-md_output/example_ramd-md.namdout\n", 382 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/examples/run_ramd_example.sh\n", 383 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/examples/run_ramd-md_example.sh\n", 384 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/examples/example_ramd_output/\n", 385 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/examples/example_ramd_output/example_ramd.namdout\n", 386 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/ramd-4.1/README\n", 387 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/alch/\n", 388 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/alch/README.txt\n", 389 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/alch/deinterleave_idws.py\n", 390 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/alch/fep.tcl\n", 391 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/colvars/\n", 392 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/colvars/test_scripted_gradients.tcl\n", 393 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/colvars/pathCV.tcl\n", 394 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/init.tcl\n", 395 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf/\n", 396 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf/vectors.tcl\n", 397 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf/abf_script.tcl\n", 398 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf/abscissa.tcl\n", 399 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf/xyDistance.tcl\n", 400 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf/distance.tcl\n", 401 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf/zCoord-1atom.tcl\n", 402 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf/distance-com.tcl\n", 403 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf/abf.tcl\n", 404 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf/pkgIndex.tcl\n", 405 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/lib/abf/zCoord.tcl\n", 406 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/notes.txt\n", 407 | "NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA/flipbinpdb\n" 408 | ] 409 | } 410 | ] 411 | }, 412 | { 413 | "cell_type": "code", 414 | "metadata": { 415 | "colab": { 416 | "base_uri": "https://localhost:8080/" 417 | }, 418 | "id": "gHL7aV_vmcuE", 419 | "outputId": "b2c07097-bb3a-4d1d-948f-e92fead730e6" 420 | }, 421 | "source": [ 422 | "#!tar -xvf 1mq5_charmm-gui_31.tgz" 423 | ], 424 | "execution_count": null, 425 | "outputs": [ 426 | { 427 | "name": "stdout", 428 | "output_type": "stream", 429 | "text": [ 430 | "charmm-gui-3159213244/1mq5.cif\n", 431 | "charmm-gui-3159213244/1mq5_hetb.crd\n", 432 | "charmm-gui-3159213244/1mq5_hetb.pdb\n", 433 | "charmm-gui-3159213244/1mq5_proa.crd\n", 434 | "charmm-gui-3159213244/1mq5_proa.pdb\n", 435 | "charmm-gui-3159213244/addCrystPdb.py\n", 436 | "charmm-gui-3159213244/checkfft.py\n", 437 | "charmm-gui-3159213244/checkfft.str\n", 438 | "charmm-gui-3159213244/crystal_image.str\n", 439 | "charmm-gui-3159213244/glycan.yml\n", 440 | "charmm-gui-3159213244/input.config.dat\n", 441 | "charmm-gui-3159213244/step1_pdbreader.crd\n", 442 | "charmm-gui-3159213244/step1_pdbreader.inp\n", 443 | "charmm-gui-3159213244/step1_pdbreader.out\n", 444 | "charmm-gui-3159213244/step1_pdbreader.pdb\n", 445 | "charmm-gui-3159213244/step1_pdbreader.psf\n", 446 | "charmm-gui-3159213244/step1_pdbreader.str\n", 447 | "charmm-gui-3159213244/step2.1_waterbox.crd\n", 448 | "charmm-gui-3159213244/step2.1_waterbox.inp\n", 449 | "charmm-gui-3159213244/step2.1_waterbox.out\n", 450 | "charmm-gui-3159213244/step2.1_waterbox.pdb\n", 451 | "charmm-gui-3159213244/step2.1_waterbox.prm\n", 452 | "charmm-gui-3159213244/step2.1_waterbox.str\n", 453 | "charmm-gui-3159213244/step2.2_ions.crd\n", 454 | "charmm-gui-3159213244/step2.2_ions.inp\n", 455 | "charmm-gui-3159213244/step2.2_ions.out\n", 456 | "charmm-gui-3159213244/step2.2_ions.pdb\n", 457 | "charmm-gui-3159213244/step2.2_ions.psf\n", 458 | "charmm-gui-3159213244/step2.2_ions.str\n", 459 | "charmm-gui-3159213244/step2.2_ions_count.str\n", 460 | "charmm-gui-3159213244/step2.2_ions_orient.crd\n", 461 | "charmm-gui-3159213244/step2_solvator.crd\n", 462 | "charmm-gui-3159213244/step2_solvator.inp\n", 463 | "charmm-gui-3159213244/step2_solvator.out\n", 464 | "charmm-gui-3159213244/step2_solvator.pdb\n", 465 | "charmm-gui-3159213244/step2_solvator.psf\n", 466 | "charmm-gui-3159213244/step2_solvator.str\n", 467 | "charmm-gui-3159213244/step3_pbcsetup.crd\n", 468 | "charmm-gui-3159213244/step3_pbcsetup.inp\n", 469 | "charmm-gui-3159213244/step3_pbcsetup.oldpsf\n", 470 | "charmm-gui-3159213244/step3_pbcsetup.out\n", 471 | "charmm-gui-3159213244/step3_pbcsetup.pdb\n", 472 | "charmm-gui-3159213244/step3_pbcsetup.psf\n", 473 | "charmm-gui-3159213244/step3_pbcsetup.str\n", 474 | "charmm-gui-3159213244/step4_equilibration.inp\n", 475 | "charmm-gui-3159213244/step5_production.inp\n", 476 | "charmm-gui-3159213244/toppar.str\n", 477 | "charmm-gui-3159213244/water_tmp.crd\n", 478 | "charmm-gui-3159213244/namd\n", 479 | "charmm-gui-3159213244/namd/step3_input.pdb\n", 480 | "charmm-gui-3159213244/namd/step5_production.inp\n", 481 | "charmm-gui-3159213244/namd/step3_input.crd\n", 482 | "charmm-gui-3159213244/namd/step3_input.psf\n", 483 | "charmm-gui-3159213244/namd/restraints\n", 484 | "charmm-gui-3159213244/namd/restraints/prot_posres.ref\n", 485 | "charmm-gui-3159213244/namd/README\n", 486 | "charmm-gui-3159213244/namd/sysinfo.dat\n", 487 | "charmm-gui-3159213244/namd/toppar\n", 488 | "charmm-gui-3159213244/namd/toppar/toppar_all36_polymer_solvent.str\n", 489 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_bacterial.str\n", 490 | "charmm-gui-3159213244/namd/toppar/toppar_all36_carb_glycolipid.str\n", 491 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_sphingo.str\n", 492 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_cholesterol.str\n", 493 | "charmm-gui-3159213244/namd/toppar/toppar_all36_prot_retinol.str\n", 494 | "charmm-gui-3159213244/namd/toppar/toppar_all36_na_rna_modified.str\n", 495 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_mycobacterial.str\n", 496 | "charmm-gui-3159213244/namd/toppar/par_all36_prot.prm\n", 497 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_lps.str\n", 498 | "charmm-gui-3159213244/namd/toppar/toppar_all36_carb_glycopeptide.str\n", 499 | "charmm-gui-3159213244/namd/toppar/par_all36_na.prm\n", 500 | "charmm-gui-3159213244/namd/toppar/toppar_all36_prot_na_combined.str\n", 501 | "charmm-gui-3159213244/namd/toppar/par_all36_cgenff.prm\n", 502 | "charmm-gui-3159213244/namd/toppar/toppar_all36_prot_c36_d_aminoacids.str\n", 503 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_miscellaneous.str\n", 504 | "charmm-gui-3159213244/namd/toppar/toppar_water_ions.str\n", 505 | "charmm-gui-3159213244/namd/toppar/xlc.prm\n", 506 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_yeast.str\n", 507 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_lnp.str\n", 508 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_detergent.str\n", 509 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_prot.str\n", 510 | "charmm-gui-3159213244/namd/toppar/toppar_all36_carb_imlab.str\n", 511 | "charmm-gui-3159213244/namd/toppar/toppar_all36_moreions.str\n", 512 | "charmm-gui-3159213244/namd/toppar/toppar_all36_nanolig_patch.str\n", 513 | "charmm-gui-3159213244/namd/toppar/toppar_all36_prot_arg0.str\n", 514 | "charmm-gui-3159213244/namd/toppar/par_interface.prm\n", 515 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_cardiolipin.str\n", 516 | "charmm-gui-3159213244/namd/toppar/toppar_dum_noble_gases.str\n", 517 | "charmm-gui-3159213244/namd/toppar/toppar_all36_prot_heme.str\n", 518 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_model.str\n", 519 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_inositol.str\n", 520 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_ether.str\n", 521 | "charmm-gui-3159213244/namd/toppar/toppar_all36_nano_lig.str\n", 522 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_archaeal.str\n", 523 | "charmm-gui-3159213244/namd/toppar/toppar_all36_synthetic_polymer_patch.str\n", 524 | "charmm-gui-3159213244/namd/toppar/toppar_all36_prot_modify_res.str\n", 525 | "charmm-gui-3159213244/namd/toppar/toppar_all36_synthetic_polymer.str\n", 526 | "charmm-gui-3159213244/namd/toppar/toppar_all36_label_spin.str\n", 527 | "charmm-gui-3159213244/namd/toppar/toppar_ions_won.str\n", 528 | "charmm-gui-3159213244/namd/toppar/par_all36_lipid.prm\n", 529 | "charmm-gui-3159213244/namd/toppar/toppar_all36_label_fluorophore.str\n", 530 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_tag.str\n", 531 | "charmm-gui-3159213244/namd/toppar/toppar_all36_prot_fluoro_alkanes.str\n", 532 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_hmmm.str\n", 533 | "charmm-gui-3159213244/namd/toppar/par_all36_carb.prm\n", 534 | "charmm-gui-3159213244/namd/toppar/toppar_all36_lipid_dag.str\n", 535 | "charmm-gui-3159213244/namd/toppar/toppar_all36_na_nad_ppi.str\n", 536 | "charmm-gui-3159213244/namd/step4_equilibration.inp\n", 537 | "charmm-gui-3159213244/toppar\n", 538 | "charmm-gui-3159213244/toppar/toppar_all36_polymer_solvent.str\n", 539 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_bacterial.str\n", 540 | "charmm-gui-3159213244/toppar/top_all36_lipid.rtf\n", 541 | "charmm-gui-3159213244/toppar/toppar_all36_carb_glycolipid.str\n", 542 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_sphingo.str\n", 543 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_cholesterol.str\n", 544 | "charmm-gui-3159213244/toppar/toppar_all36_prot_retinol.str\n", 545 | "charmm-gui-3159213244/toppar/toppar_all36_na_rna_modified.str\n", 546 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_mycobacterial.str\n", 547 | "charmm-gui-3159213244/toppar/par_all36_prot.prm\n", 548 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_lps.str\n", 549 | "charmm-gui-3159213244/toppar/top_all36_prot.rtf\n", 550 | "charmm-gui-3159213244/toppar/toppar_all36_carb_glycopeptide.str\n", 551 | "charmm-gui-3159213244/toppar/par_all36_na.prm\n", 552 | "charmm-gui-3159213244/toppar/top_interface.rtf\n", 553 | "charmm-gui-3159213244/toppar/toppar_all36_prot_na_combined.str\n", 554 | "charmm-gui-3159213244/toppar/par_all36_cgenff.prm\n", 555 | "charmm-gui-3159213244/toppar/toppar_all36_prot_c36_d_aminoacids.str\n", 556 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_miscellaneous.str\n", 557 | "charmm-gui-3159213244/toppar/toppar_all36_prot_c36m_d_aminoacids.str\n", 558 | "charmm-gui-3159213244/toppar/toppar_water_ions.str\n", 559 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_yeast.str\n", 560 | "charmm-gui-3159213244/toppar/top_all36_carb.rtf\n", 561 | "charmm-gui-3159213244/toppar/par_all36m_prot.prm\n", 562 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_lnp.str\n", 563 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_detergent.str\n", 564 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_prot.str\n", 565 | "charmm-gui-3159213244/toppar/toppar_all36_carb_imlab.str\n", 566 | "charmm-gui-3159213244/toppar/toppar_all36_moreions.str\n", 567 | "charmm-gui-3159213244/toppar/toppar_all36_nanolig_patch.str\n", 568 | "charmm-gui-3159213244/toppar/toppar_all36_prot_arg0.str\n", 569 | "charmm-gui-3159213244/toppar/par_interface.prm\n", 570 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_cardiolipin.str\n", 571 | "charmm-gui-3159213244/toppar/toppar_dum_noble_gases.str\n", 572 | "charmm-gui-3159213244/toppar/toppar_all36_prot_heme.str\n", 573 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_model.str\n", 574 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_inositol.str\n", 575 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_ether.str\n", 576 | "charmm-gui-3159213244/toppar/toppar_all36_nano_lig.str\n", 577 | "charmm-gui-3159213244/toppar/top_all36_cgenff.rtf\n", 578 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_archaeal.str\n", 579 | "charmm-gui-3159213244/toppar/toppar_all36_synthetic_polymer_patch.str\n", 580 | "charmm-gui-3159213244/toppar/toppar_all36_prot_modify_res.str\n", 581 | "charmm-gui-3159213244/toppar/toppar_all36_synthetic_polymer.str\n", 582 | "charmm-gui-3159213244/toppar/toppar_all36_label_spin.str\n", 583 | "charmm-gui-3159213244/toppar/tip216.crd\n", 584 | "charmm-gui-3159213244/toppar/toppar_ions_won.str\n", 585 | "charmm-gui-3159213244/toppar/par_all36_lipid.prm\n", 586 | "charmm-gui-3159213244/toppar/toppar_all36_label_fluorophore.str\n", 587 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_tag.str\n", 588 | "charmm-gui-3159213244/toppar/top_all36_na.rtf\n", 589 | "charmm-gui-3159213244/toppar/toppar_all36_prot_fluoro_alkanes.str\n", 590 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_hmmm.str\n", 591 | "charmm-gui-3159213244/toppar/par_all36_carb.prm\n", 592 | "charmm-gui-3159213244/toppar/toppar_all36_lipid_dag.str\n", 593 | "charmm-gui-3159213244/toppar/toppar_all36_na_nad_ppi.str\n", 594 | "charmm-gui-3159213244/xlc\n", 595 | "charmm-gui-3159213244/xlc/XLC.sdf\n", 596 | "charmm-gui-3159213244/xlc/ligandrtf.py\n", 597 | "charmm-gui-3159213244/xlc/xlc_g.rtf\n", 598 | "charmm-gui-3159213244/xlc/xlc.rtf\n", 599 | "charmm-gui-3159213244/xlc/XLC.mol2\n", 600 | "charmm-gui-3159213244/xlc/xlc.prm\n", 601 | "charmm-gui-3159213244/xlc/xlc.mol\n", 602 | "charmm-gui-3159213244/xlc/ndihe.str\n" 603 | ] 604 | } 605 | ] 606 | }, 607 | { 608 | "cell_type": "markdown", 609 | "metadata": { 610 | "id": "fqWJzHs6JCGZ" 611 | }, 612 | "source": [ 613 | "😏😁😳👍🏻**As we have mentioned, duriing the solution input generator procedure, BE Carefull of the small molecules force field seciton, if you got a halogen atom in the structure, the default one could yield error of so called LPH atom type error, which looks like the halogen atoms be protonated in a inpropriate way. You could select the \"Open MM FF\" option to avoid this error.**" 614 | ] 615 | }, 616 | { 617 | "cell_type": "code", 618 | "metadata": { 619 | "colab": { 620 | "base_uri": "https://localhost:8080/" 621 | }, 622 | "id": "6sZvujj8Cur_", 623 | "outputId": "60a2d6e9-fbdb-4713-ab07-802dd63f7713" 624 | }, 625 | "source": [ 626 | "!tar -xvf /content/charmm-gui-openMM.tgz" 627 | ], 628 | "execution_count": 5, 629 | "outputs": [ 630 | { 631 | "output_type": "stream", 632 | "name": "stdout", 633 | "text": [ 634 | "charmm-gui-3248349743/1mq5.cif\n", 635 | "charmm-gui-3248349743/1mq5_hetb.crd\n", 636 | "charmm-gui-3248349743/1mq5_hetb.pdb\n", 637 | "charmm-gui-3248349743/1mq5_proa.crd\n", 638 | "charmm-gui-3248349743/1mq5_proa.pdb\n", 639 | "charmm-gui-3248349743/addCrystPdb.py\n", 640 | "charmm-gui-3248349743/checkfft.py\n", 641 | "charmm-gui-3248349743/checkfft.str\n", 642 | "charmm-gui-3248349743/crystal_image.str\n", 643 | "charmm-gui-3248349743/glycan.yml\n", 644 | "charmm-gui-3248349743/input.config.dat\n", 645 | "charmm-gui-3248349743/step1_pdbreader.crd\n", 646 | "charmm-gui-3248349743/step1_pdbreader.inp\n", 647 | "charmm-gui-3248349743/step1_pdbreader.out\n", 648 | "charmm-gui-3248349743/step1_pdbreader.pdb\n", 649 | "charmm-gui-3248349743/step1_pdbreader.psf\n", 650 | "charmm-gui-3248349743/step1_pdbreader.str\n", 651 | "charmm-gui-3248349743/step2.1_waterbox.crd\n", 652 | "charmm-gui-3248349743/step2.1_waterbox.inp\n", 653 | "charmm-gui-3248349743/step2.1_waterbox.out\n", 654 | "charmm-gui-3248349743/step2.1_waterbox.pdb\n", 655 | "charmm-gui-3248349743/step2.1_waterbox.prm\n", 656 | "charmm-gui-3248349743/step2.1_waterbox.str\n", 657 | "charmm-gui-3248349743/step2.2_ions.crd\n", 658 | "charmm-gui-3248349743/step2.2_ions.inp\n", 659 | "charmm-gui-3248349743/step2.2_ions.out\n", 660 | "charmm-gui-3248349743/step2.2_ions.pdb\n", 661 | "charmm-gui-3248349743/step2.2_ions.psf\n", 662 | "charmm-gui-3248349743/step2.2_ions.str\n", 663 | "charmm-gui-3248349743/step2.2_ions_count.str\n", 664 | "charmm-gui-3248349743/step2.2_ions_orient.crd\n", 665 | "charmm-gui-3248349743/step2_solvator.crd\n", 666 | "charmm-gui-3248349743/step2_solvator.inp\n", 667 | "charmm-gui-3248349743/step2_solvator.out\n", 668 | "charmm-gui-3248349743/step2_solvator.pdb\n", 669 | "charmm-gui-3248349743/step2_solvator.psf\n", 670 | "charmm-gui-3248349743/step2_solvator.str\n", 671 | "charmm-gui-3248349743/step3_pbcsetup.crd\n", 672 | "charmm-gui-3248349743/step3_pbcsetup.inp\n", 673 | "charmm-gui-3248349743/step3_pbcsetup.oldpsf\n", 674 | "charmm-gui-3248349743/step3_pbcsetup.out\n", 675 | "charmm-gui-3248349743/step3_pbcsetup.pdb\n", 676 | "charmm-gui-3248349743/step3_pbcsetup.psf\n", 677 | "charmm-gui-3248349743/step3_pbcsetup.str\n", 678 | "charmm-gui-3248349743/step4_equilibration.inp\n", 679 | "charmm-gui-3248349743/step5_production.inp\n", 680 | "charmm-gui-3248349743/toppar.str\n", 681 | "charmm-gui-3248349743/water_tmp.crd\n", 682 | "charmm-gui-3248349743/namd\n", 683 | "charmm-gui-3248349743/namd/step3_input.pdb\n", 684 | "charmm-gui-3248349743/namd/step5_production.inp\n", 685 | "charmm-gui-3248349743/namd/step3_input.crd\n", 686 | "charmm-gui-3248349743/namd/step3_input.psf\n", 687 | "charmm-gui-3248349743/namd/restraints\n", 688 | "charmm-gui-3248349743/namd/restraints/prot_posres.ref\n", 689 | "charmm-gui-3248349743/namd/README\n", 690 | "charmm-gui-3248349743/namd/sysinfo.dat\n", 691 | "charmm-gui-3248349743/namd/toppar\n", 692 | "charmm-gui-3248349743/namd/toppar/toppar_all36_polymer_solvent.str\n", 693 | "charmm-gui-3248349743/namd/toppar/toppar_all36_lipid_bacterial.str\n", 694 | "charmm-gui-3248349743/namd/toppar/toppar_all36_carb_glycolipid.str\n", 695 | "charmm-gui-3248349743/namd/toppar/toppar_all36_lipid_sphingo.str\n", 696 | "charmm-gui-3248349743/namd/toppar/toppar_all36_lipid_cholesterol.str\n", 697 | "charmm-gui-3248349743/namd/toppar/toppar_all36_prot_retinol.str\n", 698 | "charmm-gui-3248349743/namd/toppar/toppar_all36_na_rna_modified.str\n", 699 | "charmm-gui-3248349743/namd/toppar/toppar_all36_lipid_mycobacterial.str\n", 700 | "charmm-gui-3248349743/namd/toppar/toppar_all36_lipid_lps.str\n", 701 | "charmm-gui-3248349743/namd/toppar/toppar_all36_carb_glycopeptide.str\n", 702 | "charmm-gui-3248349743/namd/toppar/par_all36_na.prm\n", 703 | "charmm-gui-3248349743/namd/toppar/toppar_all36_prot_na_combined.str\n", 704 | "charmm-gui-3248349743/namd/toppar/par_all36_cgenff.prm\n", 705 | "charmm-gui-3248349743/namd/toppar/toppar_all36_lipid_miscellaneous.str\n", 706 | "charmm-gui-3248349743/namd/toppar/toppar_all36_prot_c36m_d_aminoacids.str\n", 707 | "charmm-gui-3248349743/namd/toppar/toppar_water_ions.str\n", 708 | "charmm-gui-3248349743/namd/toppar/xlc.prm\n", 709 | "charmm-gui-3248349743/namd/toppar/toppar_all36_lipid_yeast.str\n", 710 | "charmm-gui-3248349743/namd/toppar/par_all36m_prot.prm\n", 711 | 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"charmm-gui-3248349743/namd/toppar/toppar_all36_lipid_ether.str\n", 725 | "charmm-gui-3248349743/namd/toppar/toppar_all36_nano_lig.str\n", 726 | "charmm-gui-3248349743/namd/toppar/toppar_all36_lipid_archaeal.str\n", 727 | "charmm-gui-3248349743/namd/toppar/toppar_all36_synthetic_polymer_patch.str\n", 728 | "charmm-gui-3248349743/namd/toppar/toppar_all36_prot_modify_res.str\n", 729 | "charmm-gui-3248349743/namd/toppar/toppar_all36_synthetic_polymer.str\n", 730 | "charmm-gui-3248349743/namd/toppar/toppar_all36_label_spin.str\n", 731 | "charmm-gui-3248349743/namd/toppar/toppar_ions_won.str\n", 732 | "charmm-gui-3248349743/namd/toppar/par_all36_lipid.prm\n", 733 | "charmm-gui-3248349743/namd/toppar/toppar_all36_label_fluorophore.str\n", 734 | "charmm-gui-3248349743/namd/toppar/toppar_all36_lipid_tag.str\n", 735 | "charmm-gui-3248349743/namd/toppar/toppar_all36_prot_fluoro_alkanes.str\n", 736 | "charmm-gui-3248349743/namd/toppar/toppar_all36_lipid_hmmm.str\n", 737 | 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"charmm-gui-3248349743/toppar/toppar_all36_lipid_lps.str\n", 752 | "charmm-gui-3248349743/toppar/top_all36_prot.rtf\n", 753 | "charmm-gui-3248349743/toppar/toppar_all36_carb_glycopeptide.str\n", 754 | "charmm-gui-3248349743/toppar/par_all36_na.prm\n", 755 | "charmm-gui-3248349743/toppar/top_interface.rtf\n", 756 | "charmm-gui-3248349743/toppar/toppar_all36_prot_na_combined.str\n", 757 | "charmm-gui-3248349743/toppar/par_all36_cgenff.prm\n", 758 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_miscellaneous.str\n", 759 | "charmm-gui-3248349743/toppar/toppar_all36_prot_c36m_d_aminoacids.str\n", 760 | "charmm-gui-3248349743/toppar/toppar_water_ions.str\n", 761 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_yeast.str\n", 762 | "charmm-gui-3248349743/toppar/top_all36_carb.rtf\n", 763 | "charmm-gui-3248349743/toppar/par_all36m_prot.prm\n", 764 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_lnp.str\n", 765 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_detergent.str\n", 766 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_prot.str\n", 767 | "charmm-gui-3248349743/toppar/toppar_all36_carb_imlab.str\n", 768 | "charmm-gui-3248349743/toppar/toppar_all36_moreions.str\n", 769 | "charmm-gui-3248349743/toppar/toppar_all36_nanolig_patch.str\n", 770 | "charmm-gui-3248349743/toppar/toppar_all36_prot_arg0.str\n", 771 | "charmm-gui-3248349743/toppar/par_interface.prm\n", 772 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_cardiolipin.str\n", 773 | "charmm-gui-3248349743/toppar/toppar_dum_noble_gases.str\n", 774 | "charmm-gui-3248349743/toppar/toppar_all36_prot_heme.str\n", 775 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_model.str\n", 776 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_inositol.str\n", 777 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_ether.str\n", 778 | "charmm-gui-3248349743/toppar/toppar_all36_nano_lig.str\n", 779 | "charmm-gui-3248349743/toppar/top_all36_cgenff.rtf\n", 780 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_archaeal.str\n", 781 | "charmm-gui-3248349743/toppar/toppar_all36_synthetic_polymer_patch.str\n", 782 | "charmm-gui-3248349743/toppar/toppar_all36_prot_modify_res.str\n", 783 | "charmm-gui-3248349743/toppar/toppar_all36_synthetic_polymer.str\n", 784 | "charmm-gui-3248349743/toppar/toppar_all36_label_spin.str\n", 785 | "charmm-gui-3248349743/toppar/tip216.crd\n", 786 | "charmm-gui-3248349743/toppar/toppar_ions_won.str\n", 787 | "charmm-gui-3248349743/toppar/par_all36_lipid.prm\n", 788 | "charmm-gui-3248349743/toppar/toppar_all36_label_fluorophore.str\n", 789 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_tag.str\n", 790 | "charmm-gui-3248349743/toppar/top_all36_na.rtf\n", 791 | "charmm-gui-3248349743/toppar/toppar_all36_prot_fluoro_alkanes.str\n", 792 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_hmmm.str\n", 793 | "charmm-gui-3248349743/toppar/par_all36_carb.prm\n", 794 | "charmm-gui-3248349743/toppar/toppar_all36_lipid_dag.str\n", 795 | "charmm-gui-3248349743/toppar/toppar_all36_na_nad_ppi.str\n", 796 | "charmm-gui-3248349743/xlc\n", 797 | "charmm-gui-3248349743/xlc/XLC.sdf\n", 798 | "charmm-gui-3248349743/xlc/ligandrtf.py\n", 799 | "charmm-gui-3248349743/xlc/xlc_g.rtf\n", 800 | "charmm-gui-3248349743/xlc/xlc.rtf\n", 801 | "charmm-gui-3248349743/xlc/XLC.mol2\n", 802 | "charmm-gui-3248349743/xlc/xlc.sdf\n", 803 | "charmm-gui-3248349743/xlc/1mq5_hetb.pdb\n", 804 | "charmm-gui-3248349743/xlc/csml_results.yml\n", 805 | "charmm-gui-3248349743/xlc/draw2graph.py\n", 806 | "charmm-gui-3248349743/xlc/xlc.prm\n", 807 | "charmm-gui-3248349743/xlc/drawing.gpickle\n", 808 | "charmm-gui-3248349743/xlc/xlc.mol\n", 809 | "charmm-gui-3248349743/xlc/drawing_3D.mol\n", 810 | "charmm-gui-3248349743/xlc/ndihe.str\n", 811 | "charmm-gui-3248349743/xlc/1mq5_hetb.mol\n", 812 | "charmm-gui-3248349743/xlc/drawing_no_h.gpickle\n" 813 | ] 814 | } 815 | ] 816 | }, 817 | { 818 | "cell_type": "code", 819 | "metadata": { 820 | "colab": { 821 | "base_uri": "https://localhost:8080/" 822 | }, 823 | "id": "AbLq1ekAES7Y", 824 | "outputId": "efad6aab-25a4-4729-c510-181b676d1ceb" 825 | }, 826 | "source": [ 827 | "I #!tar -xvf /content/1mq5_eABF.tar.gz" 828 | ], 829 | "execution_count": null, 830 | "outputs": [ 831 | { 832 | "output_type": "stream", 833 | "name": "stdout", 834 | "text": [ 835 | "._1MQ5\n", 836 | "1MQ5/\n", 837 | "1MQ5/._step2.2_ions.inp\n", 838 | "1MQ5/step2.2_ions.inp\n", 839 | "1MQ5/._step2.1_waterbox.out\n", 840 | "1MQ5/step2.1_waterbox.out\n", 841 | "1MQ5/._step2_solvator.str\n", 842 | "1MQ5/step2_solvator.str\n", 843 | "1MQ5/._step2_solvator.pdb\n", 844 | "1MQ5/step2_solvator.pdb\n", 845 | "1MQ5/._toppar.str\n", 846 | "1MQ5/toppar.str\n", 847 | "1MQ5/._step1_pdbreader.str\n", 848 | "1MQ5/step1_pdbreader.str\n", 849 | "1MQ5/._step1_pdbreader.pdb\n", 850 | "1MQ5/step1_pdbreader.pdb\n", 851 | "1MQ5/._checkfft.str\n", 852 | "1MQ5/checkfft.str\n", 853 | "1MQ5/._step1_pdbreader.psf\n", 854 | "1MQ5/step1_pdbreader.psf\n", 855 | "1MQ5/._checkfft.py\n", 856 | "1MQ5/checkfft.py\n", 857 | "1MQ5/._step5_production.inp\n", 858 | "1MQ5/step5_production.inp\n", 859 | "1MQ5/._step2_solvator.psf\n", 860 | "1MQ5/step2_solvator.psf\n", 861 | "1MQ5/._step2.1_waterbox.inp\n", 862 | "1MQ5/step2.1_waterbox.inp\n", 863 | "1MQ5/._step2.2_ions.out\n", 864 | "1MQ5/step2.2_ions.out\n", 865 | "1MQ5/._step2.2_ions_count.str\n", 866 | "1MQ5/step2.2_ions_count.str\n", 867 | "1MQ5/._water_tmp.crd\n", 868 | "1MQ5/water_tmp.crd\n", 869 | "1MQ5/._step3_pbcsetup.oldpsf\n", 870 | "1MQ5/step3_pbcsetup.oldpsf\n", 871 | "1MQ5/._step3_pbcsetup.psf\n", 872 | "1MQ5/step3_pbcsetup.psf\n", 873 | "1MQ5/._step2.2_ions.crd\n", 874 | "1MQ5/step2.2_ions.crd\n", 875 | "1MQ5/._1mq5_proa.crd\n", 876 | "1MQ5/1mq5_proa.crd\n", 877 | "1MQ5/._step2.1_waterbox.crd\n", 878 | "1MQ5/step2.1_waterbox.crd\n", 879 | "1MQ5/._step3_pbcsetup.str\n", 880 | "1MQ5/step3_pbcsetup.str\n", 881 | "1MQ5/._step3_pbcsetup.pdb\n", 882 | "1MQ5/step3_pbcsetup.pdb\n", 883 | "1MQ5/._1mq5_hetb.crd\n", 884 | "1MQ5/1mq5_hetb.crd\n", 885 | "1MQ5/._input.config.dat\n", 886 | "1MQ5/input.config.dat\n", 887 | "1MQ5/._step2.1_waterbox.prm\n", 888 | "1MQ5/step2.1_waterbox.prm\n", 889 | "1MQ5/._step3_pbcsetup.inp\n", 890 | "1MQ5/step3_pbcsetup.inp\n", 891 | "1MQ5/._step4_equilibration.inp\n", 892 | "1MQ5/step4_equilibration.inp\n", 893 | "1MQ5/._xlc\n", 894 | "1MQ5/xlc/\n", 895 | "1MQ5/eABF/\n", 896 | "1MQ5/._1mq5.cif\n", 897 | "1MQ5/1mq5.cif\n", 898 | "1MQ5/._step1_pdbreader.crd\n", 899 | "1MQ5/step1_pdbreader.crd\n", 900 | "1MQ5/._step2_solvator.crd\n", 901 | "1MQ5/step2_solvator.crd\n", 902 | "1MQ5/._step3_pbcsetup.out\n", 903 | "1MQ5/step3_pbcsetup.out\n", 904 | "1MQ5/._glycan.yml\n", 905 | "1MQ5/glycan.yml\n", 906 | "1MQ5/._namd\n", 907 | "1MQ5/namd/\n", 908 | "1MQ5/._step1_pdbreader.out\n", 909 | "1MQ5/step1_pdbreader.out\n", 910 | "1MQ5/._step2_solvator.out\n", 911 | "1MQ5/step2_solvator.out\n", 912 | "1MQ5/._1mq5_hetb.pdb\n", 913 | "1MQ5/1mq5_hetb.pdb\n", 914 | "1MQ5/._step3_pbcsetup.crd\n", 915 | "1MQ5/step3_pbcsetup.crd\n", 916 | "1MQ5/._crystal_image.str\n", 917 | "1MQ5/crystal_image.str\n", 918 | "1MQ5/._step2.1_waterbox.pdb\n", 919 | "1MQ5/step2.1_waterbox.pdb\n", 920 | "1MQ5/._step2.2_ions.psf\n", 921 | "1MQ5/step2.2_ions.psf\n", 922 | "1MQ5/._step2.1_waterbox.str\n", 923 | "1MQ5/step2.1_waterbox.str\n", 924 | "1MQ5/._addCrystPdb.py\n", 925 | "1MQ5/addCrystPdb.py\n", 926 | "1MQ5/._toppar\n", 927 | "1MQ5/toppar/\n", 928 | "1MQ5/._1mq5_proa.pdb\n", 929 | "1MQ5/1mq5_proa.pdb\n", 930 | "1MQ5/._step2.2_ions.str\n", 931 | "1MQ5/step2.2_ions.str\n", 932 | "1MQ5/._step2.2_ions.pdb\n", 933 | "1MQ5/step2.2_ions.pdb\n", 934 | "1MQ5/._step2.2_ions_orient.crd\n", 935 | "1MQ5/step2.2_ions_orient.crd\n", 936 | "1MQ5/._step2_solvator.inp\n", 937 | "1MQ5/step2_solvator.inp\n", 938 | "1MQ5/._step1_pdbreader.inp\n", 939 | "1MQ5/step1_pdbreader.inp\n", 940 | "1MQ5/toppar/._top_all36_cgenff.rtf\n", 941 | "1MQ5/toppar/top_all36_cgenff.rtf\n", 942 | "1MQ5/toppar/._par_all36_prot.prm\n", 943 | "1MQ5/toppar/par_all36_prot.prm\n", 944 | "1MQ5/toppar/._toppar_all36_prot_arg0.str\n", 945 | "1MQ5/toppar/toppar_all36_prot_arg0.str\n", 946 | "1MQ5/toppar/._toppar_all36_polymer_solvent.str\n", 947 | "1MQ5/toppar/toppar_all36_polymer_solvent.str\n", 948 | "1MQ5/toppar/._toppar_all36_nanolig_patch.str\n", 949 | "1MQ5/toppar/toppar_all36_nanolig_patch.str\n", 950 | "1MQ5/toppar/._toppar_all36_lipid_archaeal.str\n", 951 | "1MQ5/toppar/toppar_all36_lipid_archaeal.str\n", 952 | "1MQ5/toppar/._par_all36_cgenff.prm\n", 953 | "1MQ5/toppar/par_all36_cgenff.prm\n", 954 | "1MQ5/toppar/._toppar_all36_lipid_inositol.str\n", 955 | "1MQ5/toppar/toppar_all36_lipid_inositol.str\n", 956 | "1MQ5/toppar/._toppar_all36_lipid_dag.str\n", 957 | "1MQ5/toppar/toppar_all36_lipid_dag.str\n", 958 | "1MQ5/toppar/._toppar_all36_synthetic_polymer_patch.str\n", 959 | "1MQ5/toppar/toppar_all36_synthetic_polymer_patch.str\n", 960 | "1MQ5/toppar/._toppar_all36_lipid_sphingo.str\n", 961 | "1MQ5/toppar/toppar_all36_lipid_sphingo.str\n", 962 | "1MQ5/toppar/._top_all36_na.rtf\n", 963 | "1MQ5/toppar/top_all36_na.rtf\n", 964 | "1MQ5/toppar/._toppar_all36_lipid_model.str\n", 965 | "1MQ5/toppar/toppar_all36_lipid_model.str\n", 966 | "1MQ5/toppar/._toppar_all36_prot_fluoro_alkanes.str\n", 967 | "1MQ5/toppar/toppar_all36_prot_fluoro_alkanes.str\n", 968 | "1MQ5/toppar/._top_all36_carb.rtf\n", 969 | "1MQ5/toppar/top_all36_carb.rtf\n", 970 | "1MQ5/toppar/._toppar_all36_lipid_yeast.str\n", 971 | "1MQ5/toppar/toppar_all36_lipid_yeast.str\n", 972 | "1MQ5/toppar/._toppar_all36_lipid_lnp.str\n", 973 | "1MQ5/toppar/toppar_all36_lipid_lnp.str\n", 974 | "1MQ5/toppar/._toppar_all36_lipid_detergent.str\n", 975 | "1MQ5/toppar/toppar_all36_lipid_detergent.str\n", 976 | "1MQ5/toppar/._top_interface.rtf\n", 977 | "1MQ5/toppar/top_interface.rtf\n", 978 | "1MQ5/toppar/._toppar_all36_lipid_hmmm.str\n", 979 | "1MQ5/toppar/toppar_all36_lipid_hmmm.str\n", 980 | "1MQ5/toppar/._toppar_all36_prot_c36m_d_aminoacids.str\n", 981 | "1MQ5/toppar/toppar_all36_prot_c36m_d_aminoacids.str\n", 982 | "1MQ5/toppar/._top_all36_lipid.rtf\n", 983 | "1MQ5/toppar/top_all36_lipid.rtf\n", 984 | "1MQ5/toppar/._toppar_all36_carb_glycolipid.str\n", 985 | "1MQ5/toppar/toppar_all36_carb_glycolipid.str\n", 986 | "1MQ5/toppar/._par_all36_lipid.prm\n", 987 | "1MQ5/toppar/par_all36_lipid.prm\n", 988 | "1MQ5/toppar/._toppar_all36_lipid_prot.str\n", 989 | "1MQ5/toppar/toppar_all36_lipid_prot.str\n", 990 | "1MQ5/toppar/._toppar_all36_moreions.str\n", 991 | "1MQ5/toppar/toppar_all36_moreions.str\n", 992 | "1MQ5/toppar/._toppar_all36_prot_retinol.str\n", 993 | "1MQ5/toppar/toppar_all36_prot_retinol.str\n", 994 | "1MQ5/toppar/._toppar_all36_prot_heme.str\n", 995 | "1MQ5/toppar/toppar_all36_prot_heme.str\n", 996 | "1MQ5/toppar/._toppar_all36_carb_imlab.str\n", 997 | "1MQ5/toppar/toppar_all36_carb_imlab.str\n", 998 | "1MQ5/toppar/._toppar_ions_won.str\n", 999 | "1MQ5/toppar/toppar_ions_won.str\n", 1000 | "1MQ5/toppar/._toppar_all36_lipid_lps.str\n", 1001 | "1MQ5/toppar/toppar_all36_lipid_lps.str\n", 1002 | "1MQ5/toppar/._par_all36_na.prm\n", 1003 | "1MQ5/toppar/par_all36_na.prm\n", 1004 | "1MQ5/toppar/._tip216.crd\n", 1005 | "1MQ5/toppar/tip216.crd\n", 1006 | "1MQ5/toppar/._toppar_water_ions.str\n", 1007 | "1MQ5/toppar/toppar_water_ions.str\n", 1008 | "1MQ5/toppar/._toppar_all36_label_fluorophore.str\n", 1009 | "1MQ5/toppar/toppar_all36_label_fluorophore.str\n", 1010 | "1MQ5/toppar/._toppar_all36_prot_c36_d_aminoacids.str\n", 1011 | "1MQ5/toppar/toppar_all36_prot_c36_d_aminoacids.str\n", 1012 | "1MQ5/toppar/._toppar_all36_na_rna_modified.str\n", 1013 | "1MQ5/toppar/toppar_all36_na_rna_modified.str\n", 1014 | "1MQ5/toppar/._toppar_all36_synthetic_polymer.str\n", 1015 | "1MQ5/toppar/toppar_all36_synthetic_polymer.str\n", 1016 | "1MQ5/toppar/._toppar_all36_na_nad_ppi.str\n", 1017 | "1MQ5/toppar/toppar_all36_na_nad_ppi.str\n", 1018 | "1MQ5/toppar/._par_all36_carb.prm\n", 1019 | "1MQ5/toppar/par_all36_carb.prm\n", 1020 | "1MQ5/toppar/._toppar_all36_lipid_tag.str\n", 1021 | "1MQ5/toppar/toppar_all36_lipid_tag.str\n", 1022 | "1MQ5/toppar/._toppar_all36_carb_glycopeptide.str\n", 1023 | "1MQ5/toppar/toppar_all36_carb_glycopeptide.str\n", 1024 | "1MQ5/toppar/._toppar_all36_lipid_bacterial.str\n", 1025 | "1MQ5/toppar/toppar_all36_lipid_bacterial.str\n", 1026 | "1MQ5/toppar/._toppar_all36_lipid_ether.str\n", 1027 | "1MQ5/toppar/toppar_all36_lipid_ether.str\n", 1028 | "1MQ5/toppar/._par_interface.prm\n", 1029 | "1MQ5/toppar/par_interface.prm\n", 1030 | "1MQ5/toppar/._toppar_all36_label_spin.str\n", 1031 | "1MQ5/toppar/toppar_all36_label_spin.str\n", 1032 | "1MQ5/toppar/._toppar_all36_prot_modify_res.str\n", 1033 | "1MQ5/toppar/toppar_all36_prot_modify_res.str\n", 1034 | "1MQ5/toppar/._top_all36_prot.rtf\n", 1035 | "1MQ5/toppar/top_all36_prot.rtf\n", 1036 | "1MQ5/toppar/._toppar_all36_lipid_mycobacterial.str\n", 1037 | "1MQ5/toppar/toppar_all36_lipid_mycobacterial.str\n", 1038 | "1MQ5/toppar/._toppar_all36_lipid_cholesterol.str\n", 1039 | "1MQ5/toppar/toppar_all36_lipid_cholesterol.str\n", 1040 | "1MQ5/toppar/._toppar_all36_lipid_cardiolipin.str\n", 1041 | "1MQ5/toppar/toppar_all36_lipid_cardiolipin.str\n", 1042 | "1MQ5/toppar/._toppar_all36_nano_lig.str\n", 1043 | "1MQ5/toppar/toppar_all36_nano_lig.str\n", 1044 | "1MQ5/toppar/._toppar_all36_lipid_miscellaneous.str\n", 1045 | "1MQ5/toppar/toppar_all36_lipid_miscellaneous.str\n", 1046 | "1MQ5/toppar/._toppar_dum_noble_gases.str\n", 1047 | "1MQ5/toppar/toppar_dum_noble_gases.str\n", 1048 | "1MQ5/toppar/._par_all36m_prot.prm\n", 1049 | "1MQ5/toppar/par_all36m_prot.prm\n", 1050 | "1MQ5/toppar/._toppar_all36_prot_na_combined.str\n", 1051 | "1MQ5/toppar/toppar_all36_prot_na_combined.str\n", 1052 | "1MQ5/namd/._step5_8.out\n", 1053 | "1MQ5/namd/step5_8.out\n", 1054 | "1MQ5/namd/._step5_8.restart.coor\n", 1055 | "1MQ5/namd/step5_8.restart.coor\n", 1056 | "1MQ5/namd/._step5_4.xsc\n", 1057 | "1MQ5/namd/step5_4.xsc\n", 1058 | "1MQ5/namd/._step4_equilibration.vel\n", 1059 | "1MQ5/namd/step4_equilibration.vel\n", 1060 | "1MQ5/namd/._step5_10.restart.coor\n", 1061 | "1MQ5/namd/step5_10.restart.coor\n", 1062 | "1MQ5/namd/._step4_equilibration.restart.vel\n", 1063 | "1MQ5/namd/step4_equilibration.restart.vel\n", 1064 | "1MQ5/namd/._step5_5.xsc\n", 1065 | "1MQ5/namd/step5_5.xsc\n", 1066 | "1MQ5/namd/._step5_2.coor\n", 1067 | "1MQ5/namd/step5_2.coor\n", 1068 | "1MQ5/namd/._step5_9.out\n", 1069 | "1MQ5/namd/step5_9.out\n", 1070 | "1MQ5/namd/._step5_2.restart.coor.old\n", 1071 | "1MQ5/namd/step5_2.restart.coor.old\n", 1072 | "1MQ5/namd/._step5_9.dcd\n", 1073 | "1MQ5/namd/step5_9.dcd\n", 1074 | "1MQ5/namd/._step3_input.crd\n", 1075 | "1MQ5/namd/step3_input.crd\n", 1076 | "1MQ5/namd/._step4_equilibration.restart.coor\n", 1077 | "1MQ5/namd/step4_equilibration.restart.coor\n", 1078 | "1MQ5/namd/._step5_5.restart.xsc.old\n", 1079 | "1MQ5/namd/step5_5.restart.xsc.old\n", 1080 | "1MQ5/namd/._step5_7.xsc\n", 1081 | "1MQ5/namd/step5_7.xsc\n", 1082 | "1MQ5/namd/._step5_4.restart.xsc\n", 1083 | "1MQ5/namd/step5_4.restart.xsc\n", 1084 | "1MQ5/namd/._sysinfo.dat\n", 1085 | "1MQ5/namd/sysinfo.dat\n", 1086 | "1MQ5/namd/._step5_2.restart.vel\n", 1087 | "1MQ5/namd/step5_2.restart.vel\n", 1088 | "1MQ5/namd/._step5_9.restart.coor.old\n", 1089 | "1MQ5/namd/step5_9.restart.coor.old\n", 1090 | "1MQ5/namd/._step5_6.xsc\n", 1091 | "1MQ5/namd/step5_6.xsc\n", 1092 | "1MQ5/namd/._step5_8.dcd\n", 1093 | "1MQ5/namd/step5_8.dcd\n", 1094 | "1MQ5/namd/._step5_1.restart.xsc\n", 1095 | "1MQ5/namd/step5_1.restart.xsc\n", 1096 | "1MQ5/namd/._step5_2.xsc\n", 1097 | "1MQ5/namd/step5_2.xsc\n", 1098 | "1MQ5/namd/._step5_7.restart.vel.old\n", 1099 | "1MQ5/namd/step5_7.restart.vel.old\n", 1100 | "1MQ5/namd/._step5_10.out\n", 1101 | "1MQ5/namd/step5_10.out\n", 1102 | "1MQ5/namd/._step5_3.xsc\n", 1103 | "1MQ5/namd/step5_3.xsc\n", 1104 | "1MQ5/namd/._step5_2.restart.xsc.old\n", 1105 | "1MQ5/namd/step5_2.restart.xsc.old\n", 1106 | "1MQ5/namd/._step5_production.inp\n", 1107 | "1MQ5/namd/step5_production.inp\n", 1108 | "1MQ5/namd/._step5_7.restart.vel\n", 1109 | "1MQ5/namd/step5_7.restart.vel\n", 1110 | "1MQ5/namd/._step5_9.restart.coor\n", 1111 | "1MQ5/namd/step5_9.restart.coor\n", 1112 | "1MQ5/namd/._step5_8.restart.xsc\n", 1113 | "1MQ5/namd/step5_8.restart.xsc\n", 1114 | "1MQ5/namd/._step5_3.coor\n", 1115 | "1MQ5/namd/step5_3.coor\n", 1116 | "1MQ5/namd/._step5_1.xsc\n", 1117 | "1MQ5/namd/step5_1.xsc\n", 1118 | "1MQ5/namd/._step5_6.restart.coor.old\n", 1119 | "1MQ5/namd/step5_6.restart.coor.old\n", 1120 | "1MQ5/namd/._step5_10.dcd\n", 1121 | "1MQ5/namd/step5_10.dcd\n", 1122 | "1MQ5/namd/._step5_10.restart.coor.old\n", 1123 | "1MQ5/namd/step5_10.restart.coor.old\n", 1124 | "1MQ5/namd/._step5_8.restart.vel.old\n", 1125 | "1MQ5/namd/step5_8.restart.vel.old\n", 1126 | "1MQ5/namd/._step5_3.restart.coor.old\n", 1127 | "1MQ5/namd/step5_3.restart.coor.old\n", 1128 | "1MQ5/namd/._step5_4.vel\n", 1129 | "1MQ5/namd/step5_4.vel\n", 1130 | "1MQ5/namd/._step5_10.restart.xsc.old\n", 1131 | "1MQ5/namd/step5_10.restart.xsc.old\n", 1132 | "1MQ5/namd/._step5_6.restart.vel.old\n", 1133 | "1MQ5/namd/step5_6.restart.vel.old\n", 1134 | "1MQ5/namd/._step4_equilibration.xsc\n", 1135 | "1MQ5/namd/step4_equilibration.xsc\n", 1136 | "1MQ5/namd/._step5_3.restart.xsc.old\n", 1137 | "1MQ5/namd/step5_3.restart.xsc.old\n", 1138 | "1MQ5/namd/._step5_5.vel\n", 1139 | "1MQ5/namd/step5_5.vel\n", 1140 | "1MQ5/namd/._step5_8.coor\n", 1141 | "1MQ5/namd/step5_8.coor\n", 1142 | "1MQ5/namd/._step5_10.xst\n", 1143 | "1MQ5/namd/step5_10.xst\n", 1144 | "1MQ5/namd/._step5_10.coor\n", 1145 | "1MQ5/namd/step5_10.coor\n", 1146 | "1MQ5/namd/._step4_equilibration.restart.xsc\n", 1147 | "1MQ5/namd/step4_equilibration.restart.xsc\n", 1148 | "1MQ5/namd/._step5_7.vel\n", 1149 | "1MQ5/namd/step5_7.vel\n", 1150 | "1MQ5/namd/._step5_4.restart.vel\n", 1151 | "1MQ5/namd/step5_4.restart.vel\n", 1152 | "1MQ5/namd/._step5_3.restart.coor\n", 1153 | "1MQ5/namd/step5_3.restart.coor\n", 1154 | "1MQ5/namd/._step5_8.restart.coor.old\n", 1155 | "1MQ5/namd/step5_8.restart.coor.old\n", 1156 | "1MQ5/namd/._step5_4.restart.coor\n", 1157 | "1MQ5/namd/step5_4.restart.coor\n", 1158 | "1MQ5/namd/._step5_9.restart.vel.old\n", 1159 | "1MQ5/namd/step5_9.restart.vel.old\n", 1160 | "1MQ5/namd/._step5_4.coor\n", 1161 | "1MQ5/namd/step5_4.coor\n", 1162 | "1MQ5/namd/._step5_6.vel\n", 1163 | "1MQ5/namd/step5_6.vel\n", 1164 | "1MQ5/namd/._step5_2.restart.xsc\n", 1165 | "1MQ5/namd/step5_2.restart.xsc\n", 1166 | "1MQ5/namd/._step4_equilibration.coor\n", 1167 | "1MQ5/namd/step4_equilibration.coor\n", 1168 | "1MQ5/namd/._step5_2.vel\n", 1169 | "1MQ5/namd/step5_2.vel\n", 1170 | "1MQ5/namd/._step5_5.coor\n", 1171 | "1MQ5/namd/step5_5.coor\n", 1172 | "1MQ5/namd/._step5_1.restart.vel\n", 1173 | "1MQ5/namd/step5_1.restart.vel\n", 1174 | "1MQ5/namd/._step5_8.xst\n", 1175 | "1MQ5/namd/step5_8.xst\n", 1176 | "1MQ5/namd/._step5_7.restart.xsc\n", 1177 | "1MQ5/namd/step5_7.restart.xsc\n", 1178 | "1MQ5/namd/._step5_9.xst\n", 1179 | "1MQ5/namd/step5_9.xst\n", 1180 | "1MQ5/namd/._step4_equilibration.restart.vel.old\n", 1181 | "1MQ5/namd/step4_equilibration.restart.vel.old\n", 1182 | "1MQ5/namd/._step5_run.inp\n", 1183 | "1MQ5/namd/step5_run.inp\n", 1184 | "1MQ5/namd/._step5_3.vel\n", 1185 | "1MQ5/namd/step5_3.vel\n", 1186 | "1MQ5/namd/._step5_9.coor\n", 1187 | "1MQ5/namd/step5_9.coor\n", 1188 | "1MQ5/namd/._step5_1.vel\n", 1189 | "1MQ5/namd/step5_1.vel\n", 1190 | "1MQ5/namd/._step5_4.restart.xsc.old\n", 1191 | "1MQ5/namd/step5_4.restart.xsc.old\n", 1192 | "1MQ5/namd/._step5_8.restart.vel\n", 1193 | "1MQ5/namd/step5_8.restart.vel\n", 1194 | "1MQ5/namd/._step5_7.restart.coor.old\n", 1195 | "1MQ5/namd/step5_7.restart.coor.old\n", 1196 | "1MQ5/namd/._step5_1.restart.vel.old\n", 1197 | "1MQ5/namd/step5_1.restart.vel.old\n", 1198 | "1MQ5/namd/._step5_5.restart.coor\n", 1199 | "1MQ5/namd/step5_5.restart.coor\n", 1200 | "1MQ5/namd/._.step4_equilibration.out.swp\n", 1201 | "1MQ5/namd/.step4_equilibration.out.swp\n", 1202 | "1MQ5/namd/._README\n", 1203 | "1MQ5/namd/README\n", 1204 | "1MQ5/namd/._step5_2.restart.coor\n", 1205 | "1MQ5/namd/step5_2.restart.coor\n", 1206 | "1MQ5/namd/._step5_1.restart.xsc.old\n", 1207 | "1MQ5/namd/step5_1.restart.xsc.old\n", 1208 | "1MQ5/namd/._step5_7.xst\n", 1209 | "1MQ5/namd/step5_7.xst\n", 1210 | "1MQ5/namd/._step4_equilibration.inp\n", 1211 | "1MQ5/namd/step4_equilibration.inp\n", 1212 | "1MQ5/namd/._step5_9.restart.xsc\n", 1213 | "1MQ5/namd/step5_9.restart.xsc\n", 1214 | "1MQ5/namd/._step5_4.restart.vel.old\n", 1215 | "1MQ5/namd/step5_4.restart.vel.old\n", 1216 | "1MQ5/namd/._step5_6.xst\n", 1217 | "1MQ5/namd/step5_6.xst\n", 1218 | "1MQ5/namd/._step4_equilibration.restart.xsc.old\n", 1219 | "1MQ5/namd/step4_equilibration.restart.xsc.old\n", 1220 | "1MQ5/namd/._step3_input.psf\n", 1221 | "1MQ5/namd/step3_input.psf\n", 1222 | "1MQ5/namd/._step5_6.coor\n", 1223 | "1MQ5/namd/step5_6.coor\n", 1224 | "1MQ5/namd/._step5_4.xst\n", 1225 | "1MQ5/namd/step5_4.xst\n", 1226 | "1MQ5/namd/._step5_6.restart.vel\n", 1227 | "1MQ5/namd/step5_6.restart.vel\n", 1228 | "1MQ5/namd/._step5_7.restart.coor\n", 1229 | "1MQ5/namd/step5_7.restart.coor\n", 1230 | "1MQ5/namd/._step5_5.xst\n", 1231 | "1MQ5/namd/step5_5.xst\n", 1232 | "1MQ5/namd/._step5_10.vel\n", 1233 | "1MQ5/namd/step5_10.vel\n", 1234 | "1MQ5/namd/._step5_10.restart.vel\n", 1235 | "1MQ5/namd/step5_10.restart.vel\n", 1236 | "1MQ5/namd/._step5_3.restart.vel\n", 1237 | "1MQ5/namd/step5_3.restart.vel\n", 1238 | "1MQ5/namd/._step5_1.xst\n", 1239 | "1MQ5/namd/step5_1.xst\n", 1240 | "1MQ5/namd/._step5_9.restart.xsc.old\n", 1241 | "1MQ5/namd/step5_9.restart.xsc.old\n", 1242 | "1MQ5/namd/._step3_input.str\n", 1243 | "1MQ5/namd/step3_input.str\n", 1244 | "1MQ5/namd/._step3_input.pdb\n", 1245 | "1MQ5/namd/step3_input.pdb\n", 1246 | "1MQ5/namd/._step4_equilibration.dcd\n", 1247 | "1MQ5/namd/step4_equilibration.dcd\n", 1248 | "1MQ5/namd/._step5_4.restart.coor.old\n", 1249 | "1MQ5/namd/step5_4.restart.coor.old\n", 1250 | "1MQ5/namd/._step5_7.coor\n", 1251 | "1MQ5/namd/step5_7.coor\n", 1252 | "1MQ5/namd/._step5_5.restart.xsc\n", 1253 | "1MQ5/namd/step5_5.restart.xsc\n", 1254 | "1MQ5/namd/._step5_6.restart.coor\n", 1255 | "1MQ5/namd/step5_6.restart.coor\n", 1256 | "1MQ5/namd/._step5_8.vel\n", 1257 | "1MQ5/namd/step5_8.vel\n", 1258 | "1MQ5/namd/._step5_1.restart.coor\n", 1259 | "1MQ5/namd/step5_1.restart.coor\n", 1260 | "1MQ5/namd/._step5_2.xst\n", 1261 | "1MQ5/namd/step5_2.xst\n", 1262 | "1MQ5/namd/._step5_3.restart.vel.old\n", 1263 | "1MQ5/namd/step5_3.restart.vel.old\n", 1264 | "1MQ5/namd/._step4_equilibration.out\n", 1265 | "1MQ5/namd/step4_equilibration.out\n", 1266 | "1MQ5/namd/._restraints\n", 1267 | "1MQ5/namd/restraints/\n", 1268 | "1MQ5/namd/._step5_3.xst\n", 1269 | "1MQ5/namd/step5_3.xst\n", 1270 | "1MQ5/namd/._step5_9.vel\n", 1271 | "1MQ5/namd/step5_9.vel\n", 1272 | "1MQ5/namd/._step5_10.restart.vel.old\n", 1273 | "1MQ5/namd/step5_10.restart.vel.old\n", 1274 | "1MQ5/namd/._step5_6.restart.xsc.old\n", 1275 | "1MQ5/namd/step5_6.restart.xsc.old\n", 1276 | "1MQ5/namd/._step5_3.dcd\n", 1277 | "1MQ5/namd/step5_3.dcd\n", 1278 | "1MQ5/namd/._step5_8.restart.xsc.old\n", 1279 | "1MQ5/namd/step5_8.restart.xsc.old\n", 1280 | "1MQ5/namd/._step5_1.out\n", 1281 | "1MQ5/namd/step5_1.out\n", 1282 | "1MQ5/namd/._run.csh\n", 1283 | "1MQ5/namd/run.csh\n", 1284 | "1MQ5/namd/._step5_9.restart.vel\n", 1285 | "1MQ5/namd/step5_9.restart.vel\n", 1286 | "1MQ5/namd/._step5_2.dcd\n", 1287 | "1MQ5/namd/step5_2.dcd\n", 1288 | "1MQ5/namd/._step5_2.restart.vel.old\n", 1289 | "1MQ5/namd/step5_2.restart.vel.old\n", 1290 | "1MQ5/namd/._step5_2.out\n", 1291 | "1MQ5/namd/step5_2.out\n", 1292 | "1MQ5/namd/._step5_6.restart.xsc\n", 1293 | "1MQ5/namd/step5_6.restart.xsc\n", 1294 | "1MQ5/namd/._step4_equilibration.xst\n", 1295 | "1MQ5/namd/step4_equilibration.xst\n", 1296 | "1MQ5/namd/._step5_10.restart.xsc\n", 1297 | "1MQ5/namd/step5_10.restart.xsc\n", 1298 | "1MQ5/namd/._step5_7.restart.xsc.old\n", 1299 | "1MQ5/namd/step5_7.restart.xsc.old\n", 1300 | "1MQ5/namd/._step5_1.restart.coor.old\n", 1301 | "1MQ5/namd/step5_1.restart.coor.old\n", 1302 | "1MQ5/namd/._step5_10.xsc\n", 1303 | "1MQ5/namd/step5_10.xsc\n", 1304 | "1MQ5/namd/._step5_3.out\n", 1305 | "1MQ5/namd/step5_3.out\n", 1306 | "1MQ5/namd/._step5_1.dcd\n", 1307 | "1MQ5/namd/step5_1.dcd\n", 1308 | "1MQ5/namd/._step5_5.dcd\n", 1309 | "1MQ5/namd/step5_5.dcd\n", 1310 | "1MQ5/namd/._step5_7.out\n", 1311 | "1MQ5/namd/step5_7.out\n", 1312 | "1MQ5/namd/._step5_3.restart.xsc\n", 1313 | "1MQ5/namd/step5_3.restart.xsc\n", 1314 | "1MQ5/namd/._toppar\n", 1315 | "1MQ5/namd/toppar/\n", 1316 | "1MQ5/namd/._step5_5.restart.coor.old\n", 1317 | "1MQ5/namd/step5_5.restart.coor.old\n", 1318 | "1MQ5/namd/._step5_5.restart.vel\n", 1319 | "1MQ5/namd/step5_5.restart.vel\n", 1320 | "1MQ5/namd/._FFTW_NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA.txt\n", 1321 | "1MQ5/namd/FFTW_NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA.txt\n", 1322 | "1MQ5/namd/._step4_equilibration.restart.coor.old\n", 1323 | "1MQ5/namd/step4_equilibration.restart.coor.old\n", 1324 | "1MQ5/namd/._step5_6.out\n", 1325 | "1MQ5/namd/step5_6.out\n", 1326 | "1MQ5/namd/._step5_5.restart.vel.old\n", 1327 | "1MQ5/namd/step5_5.restart.vel.old\n", 1328 | "1MQ5/namd/._step5_4.dcd\n", 1329 | "1MQ5/namd/step5_4.dcd\n", 1330 | "1MQ5/namd/._step5_6.dcd\n", 1331 | "1MQ5/namd/step5_6.dcd\n", 1332 | "1MQ5/namd/._step5_4.out\n", 1333 | "1MQ5/namd/step5_4.out\n", 1334 | "1MQ5/namd/._step5_8.xsc\n", 1335 | "1MQ5/namd/step5_8.xsc\n", 1336 | "1MQ5/namd/._step5_9.xsc\n", 1337 | "1MQ5/namd/step5_9.xsc\n", 1338 | "1MQ5/namd/._step5_1.coor\n", 1339 | "1MQ5/namd/step5_1.coor\n", 1340 | "1MQ5/namd/._step5_5.out\n", 1341 | "1MQ5/namd/step5_5.out\n", 1342 | "1MQ5/namd/._step5_7.dcd\n", 1343 | "1MQ5/namd/step5_7.dcd\n", 1344 | "1MQ5/namd/toppar/._par_all36_prot.prm\n", 1345 | "1MQ5/namd/toppar/par_all36_prot.prm\n", 1346 | "1MQ5/namd/toppar/._toppar_all36_prot_arg0.str\n", 1347 | "1MQ5/namd/toppar/toppar_all36_prot_arg0.str\n", 1348 | "1MQ5/namd/toppar/._toppar_all36_polymer_solvent.str\n", 1349 | "1MQ5/namd/toppar/toppar_all36_polymer_solvent.str\n", 1350 | "1MQ5/namd/toppar/._toppar_all36_nanolig_patch.str\n", 1351 | "1MQ5/namd/toppar/toppar_all36_nanolig_patch.str\n", 1352 | "1MQ5/namd/toppar/._toppar_all36_lipid_archaeal.str\n", 1353 | "1MQ5/namd/toppar/toppar_all36_lipid_archaeal.str\n", 1354 | "1MQ5/namd/toppar/._par_all36_cgenff.prm\n", 1355 | "1MQ5/namd/toppar/par_all36_cgenff.prm\n", 1356 | "1MQ5/namd/toppar/._toppar_all36_lipid_inositol.str\n", 1357 | "1MQ5/namd/toppar/toppar_all36_lipid_inositol.str\n", 1358 | "1MQ5/namd/toppar/._toppar_all36_lipid_dag.str\n", 1359 | "1MQ5/namd/toppar/toppar_all36_lipid_dag.str\n", 1360 | "1MQ5/namd/toppar/._toppar_all36_synthetic_polymer_patch.str\n", 1361 | "1MQ5/namd/toppar/toppar_all36_synthetic_polymer_patch.str\n", 1362 | "1MQ5/namd/toppar/._toppar_all36_lipid_sphingo.str\n", 1363 | "1MQ5/namd/toppar/toppar_all36_lipid_sphingo.str\n", 1364 | "1MQ5/namd/toppar/._toppar_all36_lipid_model.str\n", 1365 | "1MQ5/namd/toppar/toppar_all36_lipid_model.str\n", 1366 | "1MQ5/namd/toppar/._toppar_all36_prot_fluoro_alkanes.str\n", 1367 | "1MQ5/namd/toppar/toppar_all36_prot_fluoro_alkanes.str\n", 1368 | "1MQ5/namd/toppar/._toppar_all36_lipid_yeast.str\n", 1369 | "1MQ5/namd/toppar/toppar_all36_lipid_yeast.str\n", 1370 | "1MQ5/namd/toppar/._toppar_all36_lipid_lnp.str\n", 1371 | "1MQ5/namd/toppar/toppar_all36_lipid_lnp.str\n", 1372 | "1MQ5/namd/toppar/._toppar_all36_lipid_detergent.str\n", 1373 | "1MQ5/namd/toppar/toppar_all36_lipid_detergent.str\n", 1374 | "1MQ5/namd/toppar/._toppar_all36_lipid_hmmm.str\n", 1375 | "1MQ5/namd/toppar/toppar_all36_lipid_hmmm.str\n", 1376 | "1MQ5/namd/toppar/._toppar_all36_carb_glycolipid.str\n", 1377 | "1MQ5/namd/toppar/toppar_all36_carb_glycolipid.str\n", 1378 | "1MQ5/namd/toppar/._par_all36_lipid.prm\n", 1379 | "1MQ5/namd/toppar/par_all36_lipid.prm\n", 1380 | "1MQ5/namd/toppar/._toppar_all36_lipid_prot.str\n", 1381 | "1MQ5/namd/toppar/toppar_all36_lipid_prot.str\n", 1382 | "1MQ5/namd/toppar/._toppar_all36_moreions.str\n", 1383 | "1MQ5/namd/toppar/toppar_all36_moreions.str\n", 1384 | "1MQ5/namd/toppar/._toppar_all36_prot_retinol.str\n", 1385 | "1MQ5/namd/toppar/toppar_all36_prot_retinol.str\n", 1386 | "1MQ5/namd/toppar/._toppar_all36_prot_heme.str\n", 1387 | "1MQ5/namd/toppar/toppar_all36_prot_heme.str\n", 1388 | "1MQ5/namd/toppar/._toppar_all36_carb_imlab.str\n", 1389 | "1MQ5/namd/toppar/toppar_all36_carb_imlab.str\n", 1390 | "1MQ5/namd/toppar/._toppar_ions_won.str\n", 1391 | "1MQ5/namd/toppar/toppar_ions_won.str\n", 1392 | "1MQ5/namd/toppar/._toppar_all36_lipid_lps.str\n", 1393 | "1MQ5/namd/toppar/toppar_all36_lipid_lps.str\n", 1394 | "1MQ5/namd/toppar/._par_all36_na.prm\n", 1395 | "1MQ5/namd/toppar/par_all36_na.prm\n", 1396 | "1MQ5/namd/toppar/._toppar_water_ions.str\n", 1397 | "1MQ5/namd/toppar/toppar_water_ions.str\n", 1398 | "1MQ5/namd/toppar/._xlc.prm\n", 1399 | "1MQ5/namd/toppar/xlc.prm\n", 1400 | "1MQ5/namd/toppar/._toppar_all36_label_fluorophore.str\n", 1401 | "1MQ5/namd/toppar/toppar_all36_label_fluorophore.str\n", 1402 | "1MQ5/namd/toppar/._toppar_all36_prot_c36_d_aminoacids.str\n", 1403 | "1MQ5/namd/toppar/toppar_all36_prot_c36_d_aminoacids.str\n", 1404 | "1MQ5/namd/toppar/._toppar_all36_na_rna_modified.str\n", 1405 | "1MQ5/namd/toppar/toppar_all36_na_rna_modified.str\n", 1406 | "1MQ5/namd/toppar/._toppar_all36_synthetic_polymer.str\n", 1407 | "1MQ5/namd/toppar/toppar_all36_synthetic_polymer.str\n", 1408 | "1MQ5/namd/toppar/._toppar_all36_na_nad_ppi.str\n", 1409 | "1MQ5/namd/toppar/toppar_all36_na_nad_ppi.str\n", 1410 | "1MQ5/namd/toppar/._par_all36_carb.prm\n", 1411 | "1MQ5/namd/toppar/par_all36_carb.prm\n", 1412 | "1MQ5/namd/toppar/._toppar_all36_lipid_tag.str\n", 1413 | "1MQ5/namd/toppar/toppar_all36_lipid_tag.str\n", 1414 | "1MQ5/namd/toppar/._toppar_all36_carb_glycopeptide.str\n", 1415 | "1MQ5/namd/toppar/toppar_all36_carb_glycopeptide.str\n", 1416 | "1MQ5/namd/toppar/._toppar_all36_lipid_bacterial.str\n", 1417 | "1MQ5/namd/toppar/toppar_all36_lipid_bacterial.str\n", 1418 | "1MQ5/namd/toppar/._toppar_all36_lipid_ether.str\n", 1419 | "1MQ5/namd/toppar/toppar_all36_lipid_ether.str\n", 1420 | "1MQ5/namd/toppar/._par_interface.prm\n", 1421 | "1MQ5/namd/toppar/par_interface.prm\n", 1422 | "1MQ5/namd/toppar/._toppar_all36_label_spin.str\n", 1423 | "1MQ5/namd/toppar/toppar_all36_label_spin.str\n", 1424 | "1MQ5/namd/toppar/._toppar_all36_prot_modify_res.str\n", 1425 | "1MQ5/namd/toppar/toppar_all36_prot_modify_res.str\n", 1426 | "1MQ5/namd/toppar/._toppar_all36_lipid_mycobacterial.str\n", 1427 | "1MQ5/namd/toppar/toppar_all36_lipid_mycobacterial.str\n", 1428 | "1MQ5/namd/toppar/._toppar_all36_lipid_cholesterol.str\n", 1429 | "1MQ5/namd/toppar/toppar_all36_lipid_cholesterol.str\n", 1430 | "1MQ5/namd/toppar/._toppar_all36_lipid_cardiolipin.str\n", 1431 | "1MQ5/namd/toppar/toppar_all36_lipid_cardiolipin.str\n", 1432 | "1MQ5/namd/toppar/._toppar_all36_nano_lig.str\n", 1433 | "1MQ5/namd/toppar/toppar_all36_nano_lig.str\n", 1434 | "1MQ5/namd/toppar/._toppar_all36_lipid_miscellaneous.str\n", 1435 | "1MQ5/namd/toppar/toppar_all36_lipid_miscellaneous.str\n", 1436 | "1MQ5/namd/toppar/._toppar_dum_noble_gases.str\n", 1437 | "1MQ5/namd/toppar/toppar_dum_noble_gases.str\n", 1438 | "1MQ5/namd/toppar/._toppar_all36_prot_na_combined.str\n", 1439 | "1MQ5/namd/toppar/toppar_all36_prot_na_combined.str\n", 1440 | "1MQ5/namd/restraints/._prot_posres.ref\n", 1441 | "1MQ5/namd/restraints/prot_posres.ref\n", 1442 | "1MQ5/eABF/._par_all36_prot.prm\n", 1443 | "1MQ5/eABF/par_all36_prot.prm\n", 1444 | "1MQ5/eABF/._par_all36_cgenff.prm\n", 1445 | "1MQ5/eABF/par_all36_cgenff.prm\n", 1446 | "1MQ5/eABF/._bound.psf\n", 1447 | "1MQ5/eABF/bound.psf\n", 1448 | "1MQ5/eABF/bound.pdb\n", 1449 | "1MQ5/eABF/eq.xsc\n", 1450 | "1MQ5/eABF/._par_all36_lipid.prm\n", 1451 | "1MQ5/eABF/par_all36_lipid.prm\n", 1452 | "1MQ5/eABF/001_RMSD_bound/\n", 1453 | "1MQ5/eABF/eq_normalized.xst\n", 1454 | "1MQ5/eABF/._par_all36_na.prm\n", 1455 | "1MQ5/eABF/par_all36_na.prm\n", 1456 | "1MQ5/eABF/._eq.vel\n", 1457 | "1MQ5/eABF/eq.vel\n", 1458 | "1MQ5/eABF/._xlc.prm\n", 1459 | "1MQ5/eABF/xlc.prm\n", 1460 | "1MQ5/eABF/._par_all36_carb.prm\n", 1461 | "1MQ5/eABF/par_all36_carb.prm\n", 1462 | "1MQ5/eABF/CVs.tcl\n", 1463 | "1MQ5/eABF/002_euler_theta/\n", 1464 | "1MQ5/eABF/008_RMSD_unbound/\n", 1465 | "1MQ5/eABF/003_euler_phi/\n", 1466 | "1MQ5/eABF/._par_interface.prm\n", 1467 | "1MQ5/eABF/par_interface.prm\n", 1468 | "1MQ5/eABF/eq.coor\n", 1469 | "1MQ5/eABF/alter_alchemy/\n", 1470 | "1MQ5/eABF/eq_normalized.coor\n", 1471 | "1MQ5/eABF/007_r/\n", 1472 | "1MQ5/eABF/006_polar_phi/\n", 1473 | "1MQ5/eABF/004_euler_psi/\n", 1474 | "1MQ5/eABF/005_polar_theta/\n", 1475 | "1MQ5/eABF/._par_all36m_prot.prm\n", 1476 | "1MQ5/eABF/par_all36m_prot.prm\n", 1477 | "1MQ5/eABF/005_polar_theta/abf.conf\n", 1478 | "1MQ5/eABF/005_polar_theta/abf_restart.conf\n", 1479 | "1MQ5/eABF/005_polar_theta/output/\n", 1480 | "1MQ5/eABF/005_polar_theta/ligand.pdb\n", 1481 | "1MQ5/eABF/005_polar_theta/colvar.in\n", 1482 | "1MQ5/eABF/005_polar_theta/protein.pdb\n", 1483 | "1MQ5/eABF/004_euler_psi/abf.conf\n", 1484 | "1MQ5/eABF/004_euler_psi/abf_restart.conf\n", 1485 | "1MQ5/eABF/004_euler_psi/output/\n", 1486 | "1MQ5/eABF/004_euler_psi/ligand.pdb\n", 1487 | "1MQ5/eABF/004_euler_psi/colvar.in\n", 1488 | "1MQ5/eABF/004_euler_psi/protein.pdb\n", 1489 | "1MQ5/eABF/006_polar_phi/abf.conf\n", 1490 | "1MQ5/eABF/006_polar_phi/abf_restart.conf\n", 1491 | "1MQ5/eABF/006_polar_phi/output/\n", 1492 | "1MQ5/eABF/006_polar_phi/ligand.pdb\n", 1493 | "1MQ5/eABF/006_polar_phi/colvar.in\n", 1494 | "1MQ5/eABF/006_polar_phi/protein.pdb\n", 1495 | "1MQ5/eABF/007_r/solvated.pdb\n", 1496 | "1MQ5/eABF/007_r/._bound.psf\n", 1497 | "1MQ5/eABF/007_r/bound.psf\n", 1498 | "1MQ5/eABF/007_r/abf.conf\n", 1499 | "1MQ5/eABF/007_r/solvated.psf\n", 1500 | "1MQ5/eABF/007_r/abf_restart.conf\n", 1501 | "1MQ5/eABF/007_r/solvated.log\n", 1502 | "1MQ5/eABF/007_r/output/\n", 1503 | "1MQ5/eABF/007_r/ligand.pdb\n", 1504 | "1MQ5/eABF/007_r/bound.coor\n", 1505 | "1MQ5/eABF/007_r/colvar.in\n", 1506 | "1MQ5/eABF/007_r/protein.pdb\n", 1507 | "1MQ5/eABF/007_r/bound.coor.pdb\n", 1508 | "1MQ5/eABF/alter_alchemy/bound_genAtom.conf\n", 1509 | "1MQ5/eABF/alter_alchemy/fep.fep\n", 1510 | "1MQ5/eABF/alter_alchemy/bound_annihRestraint.in\n", 1511 | "1MQ5/eABF/alter_alchemy/unbound_genAtom.conf\n", 1512 | "1MQ5/eABF/alter_alchemy/unbound_annihRestraint.in\n", 1513 | "1MQ5/eABF/alter_alchemy/unbound_annihAtom.conf\n", 1514 | "1MQ5/eABF/alter_alchemy/output/\n", 1515 | "1MQ5/eABF/alter_alchemy/unbound_genAtom.in\n", 1516 | "1MQ5/eABF/alter_alchemy/ligand.pdb\n", 1517 | "1MQ5/eABF/alter_alchemy/bound_genRestraint.in\n", 1518 | "1MQ5/eABF/alter_alchemy/bound_genRestraint.conf\n", 1519 | "1MQ5/eABF/alter_alchemy/unbound_genRestraint.in\n", 1520 | "1MQ5/eABF/alter_alchemy/bound_genAtom.in\n", 1521 | "1MQ5/eABF/alter_alchemy/unbound_genRestraint.conf\n", 1522 | "1MQ5/eABF/alter_alchemy/bound_annihAtom.conf\n", 1523 | "1MQ5/eABF/alter_alchemy/unbound.pdb\n", 1524 | "1MQ5/eABF/alter_alchemy/unbound_annihRestraint.conf\n", 1525 | "1MQ5/eABF/alter_alchemy/fep_unbound.fep\n", 1526 | "1MQ5/eABF/alter_alchemy/ligand_unbound.pdb\n", 1527 | "1MQ5/eABF/alter_alchemy/unbound.psf\n", 1528 | "1MQ5/eABF/alter_alchemy/protein.pdb\n", 1529 | "1MQ5/eABF/alter_alchemy/bound_annihRestraint.conf\n", 1530 | "1MQ5/eABF/003_euler_phi/abf.conf\n", 1531 | "1MQ5/eABF/003_euler_phi/abf_restart.conf\n", 1532 | "1MQ5/eABF/003_euler_phi/output/\n", 1533 | "1MQ5/eABF/003_euler_phi/ligand.pdb\n", 1534 | "1MQ5/eABF/003_euler_phi/colvar.in\n", 1535 | "1MQ5/eABF/003_euler_phi/protein.pdb\n", 1536 | "1MQ5/eABF/008_RMSD_unbound/lig.pdb\n", 1537 | "1MQ5/eABF/008_RMSD_unbound/._bound.psf\n", 1538 | "1MQ5/eABF/008_RMSD_unbound/bound.psf\n", 1539 | "1MQ5/eABF/008_RMSD_unbound/abf.conf\n", 1540 | "1MQ5/eABF/008_RMSD_unbound/lig.psf\n", 1541 | "1MQ5/eABF/008_RMSD_unbound/abf_restart.conf\n", 1542 | "1MQ5/eABF/008_RMSD_unbound/output/\n", 1543 | "1MQ5/eABF/008_RMSD_unbound/ligand.pdb\n", 1544 | "1MQ5/eABF/008_RMSD_unbound/bound.coor\n", 1545 | "1MQ5/eABF/008_RMSD_unbound/colvar.in\n", 1546 | "1MQ5/eABF/008_RMSD_unbound/protein.pdb\n", 1547 | "1MQ5/eABF/002_euler_theta/abf.conf\n", 1548 | "1MQ5/eABF/002_euler_theta/abf_restart.conf\n", 1549 | "1MQ5/eABF/002_euler_theta/output/\n", 1550 | "1MQ5/eABF/002_euler_theta/ligand.pdb\n", 1551 | "1MQ5/eABF/002_euler_theta/colvar.in\n", 1552 | "1MQ5/eABF/002_euler_theta/protein.pdb\n", 1553 | "1MQ5/eABF/001_RMSD_bound/abf.conf\n", 1554 | "1MQ5/eABF/001_RMSD_bound/abf_restart.conf\n", 1555 | "1MQ5/eABF/001_RMSD_bound/output/\n", 1556 | "1MQ5/eABF/001_RMSD_bound/ligand.pdb\n", 1557 | "1MQ5/eABF/001_RMSD_bound/colvar.in\n", 1558 | "1MQ5/eABF/001_RMSD_bound/protein.pdb\n", 1559 | "1MQ5/xlc/._xlc.mol\n", 1560 | "1MQ5/xlc/xlc.mol\n", 1561 | "1MQ5/xlc/._xlc_g.rtf\n", 1562 | "1MQ5/xlc/xlc_g.rtf\n", 1563 | "1MQ5/xlc/._ndihe.str\n", 1564 | "1MQ5/xlc/ndihe.str\n", 1565 | "1MQ5/xlc/._ligandrtf.py\n", 1566 | "1MQ5/xlc/ligandrtf.py\n", 1567 | "1MQ5/xlc/._xlc.prm\n", 1568 | "1MQ5/xlc/xlc.prm\n", 1569 | "1MQ5/xlc/._XLC.mol2\n", 1570 | "1MQ5/xlc/XLC.mol2\n", 1571 | "1MQ5/xlc/._XLC.sdf\n", 1572 | "1MQ5/xlc/XLC.sdf\n", 1573 | "1MQ5/xlc/._xlc.rtf\n", 1574 | "1MQ5/xlc/xlc.rtf\n" 1575 | ] 1576 | } 1577 | ] 1578 | }, 1579 | { 1580 | "cell_type": "markdown", 1581 | "metadata": { 1582 | "id": "OpHQwDttoppi" 1583 | }, 1584 | "source": [ 1585 | "**手动修改namd3 路径为/content/NAMD_3.0xxxx/namd3**\n" 1586 | ] 1587 | }, 1588 | { 1589 | "cell_type": "code", 1590 | "metadata": { 1591 | "colab": { 1592 | "base_uri": "https://localhost:8080/" 1593 | }, 1594 | "id": "Jb3QhfFqozi0", 1595 | "outputId": "1e81ff66-ca7f-4168-d21e-48eb0b6777f9" 1596 | }, 1597 | "source": [ 1598 | "#%cd /content/charmm-gui-3159213244/namd" 1599 | ], 1600 | "execution_count": null, 1601 | "outputs": [ 1602 | { 1603 | "name": "stdout", 1604 | "output_type": "stream", 1605 | "text": [ 1606 | "/content/charmm-gui-3159213244/namd\n" 1607 | ] 1608 | } 1609 | ] 1610 | }, 1611 | { 1612 | "cell_type": "code", 1613 | "metadata": { 1614 | "colab": { 1615 | "base_uri": "https://localhost:8080/" 1616 | }, 1617 | "id": "dz7ZE6DgC-Z-", 1618 | "outputId": "751f686b-23b0-47d5-9d2b-7a09bc33e8ce" 1619 | }, 1620 | "source": [ 1621 | "%cd /content/charmm-gui-3248349743/namd" 1622 | ], 1623 | "execution_count": 6, 1624 | "outputs": [ 1625 | { 1626 | "output_type": "stream", 1627 | "name": "stdout", 1628 | "text": [ 1629 | "/content/charmm-gui-3248349743/namd\n" 1630 | ] 1631 | } 1632 | ] 1633 | }, 1634 | { 1635 | "cell_type": "code", 1636 | "metadata": { 1637 | "colab": { 1638 | "base_uri": "https://localhost:8080/" 1639 | }, 1640 | "id": "MEHCeochEcu-", 1641 | "outputId": "3c42b56e-c241-4e34-d2d6-d23de4295a30" 1642 | }, 1643 | "source": [ 1644 | "#%cd /content/1MQ5/eABF" 1645 | ], 1646 | "execution_count": null, 1647 | "outputs": [ 1648 | { 1649 | "output_type": "stream", 1650 | "name": "stdout", 1651 | "text": [ 1652 | "/content/1MQ5/eABF\n" 1653 | ] 1654 | } 1655 | ] 1656 | }, 1657 | { 1658 | "cell_type": "markdown", 1659 | "metadata": { 1660 | "id": "s5KuaWeHHT87" 1661 | }, 1662 | "source": [ 1663 | "⚠️ 从github上下载一个拓扑文件补丁，并把该补丁的路径写入conf文件中，这些都需要手动完成。或者直接上传一个完整的拓扑文件包然后解压并放置到正确的路径。" 1664 | ] 1665 | }, 1666 | { 1667 | "cell_type": "code", 1668 | "metadata": { 1669 | "id": "C27AtttaFlqn" 1670 | }, 1671 | "source": [ 1672 | "!cp /content/drive/MyDrive/Colab谷歌计算平台50美元算力测试/toppar_water_ions.mod.str /content/charmm-gui-3248349743/namd/toppar" 1673 | ], 1674 | "execution_count": 7, 1675 | "outputs": [] 1676 | }, 1677 | { 1678 | "cell_type": "code", 1679 | "metadata": { 1680 | "colab": { 1681 | "base_uri": "https://localhost:8080/" 1682 | }, 1683 | "id": "zR9GaOdoGomz", 1684 | "outputId": "1a922f1b-a396-409b-d42b-d09135ea6c23" 1685 | }, 1686 | "source": [ 1687 | "#!wget https://github.com/quantaosun/NAMD-FEP/blob/main/toppar_water_ions.mod.str" 1688 | ], 1689 | "execution_count": null, 1690 | "outputs": [ 1691 | { 1692 | "output_type": "stream", 1693 | "name": "stdout", 1694 | "text": [ 1695 | "--2021-09-15 09:42:18-- https://github.com/quantaosun/NAMD-FEP/blob/main/toppar_water_ions.mod.str\n", 1696 | "Resolving github.com (github.com)... 140.82.121.3\n", 1697 | "Connecting to github.com (github.com)|140.82.121.3|:443... connected.\n", 1698 | "HTTP request sent, awaiting response... 200 OK\n", 1699 | "Length: unspecified [text/html]\n", 1700 | "Saving to: ‘toppar_water_ions.mod.str’\n", 1701 | "\n", 1702 | "toppar_water_ions.m [ <=> ] 165.47K --.-KB/s in 0.03s \n", 1703 | "\n", 1704 | "2021-09-15 09:42:19 (5.31 MB/s) - ‘toppar_water_ions.mod.str’ saved [169444]\n", 1705 | "\n" 1706 | ] 1707 | } 1708 | ] 1709 | }, 1710 | { 1711 | "cell_type": "code", 1712 | "metadata": { 1713 | "colab": { 1714 | "base_uri": "https://localhost:8080/" 1715 | }, 1716 | "id": "MRGk96nHI19-", 1717 | "outputId": "b9ca2dc1-f11c-4801-fd80-e17ad82cbfaa" 1718 | }, 1719 | "source": [ 1720 | "#!wget https://github.com/quantaosun/NAMD-FEP/blob/main/toppar_all36_prot_na_combined.str" 1721 | ], 1722 | "execution_count": null, 1723 | "outputs": [ 1724 | { 1725 | "output_type": "stream", 1726 | "name": "stdout", 1727 | "text": [ 1728 | "--2021-09-15 06:28:09-- https://github.com/quantaosun/NAMD-FEP/blob/main/toppar_all36_prot_na_combined.str\n", 1729 | "Resolving github.com (github.com)... 140.82.121.4\n", 1730 | "Connecting to github.com (github.com)|140.82.121.4|:443... connected.\n", 1731 | "HTTP request sent, awaiting response... 200 OK\n", 1732 | "Length: unspecified [text/html]\n", 1733 | "Saving to: ‘toppar_all36_prot_na_combined.str’\n", 1734 | "\n", 1735 | "toppar_all36_prot_n [ <=> ] 548.00K --.-KB/s in 0.04s \n", 1736 | "\n", 1737 | "2021-09-15 06:28:10 (13.7 MB/s) - ‘toppar_all36_prot_na_combined.str’ saved [561155]\n", 1738 | "\n" 1739 | ] 1740 | } 1741 | ] 1742 | }, 1743 | { 1744 | "cell_type": "code", 1745 | "metadata": { 1746 | "id": "CTRXy9Ef5ZVM" 1747 | }, 1748 | "source": [ 1749 | "#!cp /content/toppar_all36_prot_na_combined.str /content/1MQ5/eABF" 1750 | ], 1751 | "execution_count": null, 1752 | "outputs": [] 1753 | }, 1754 | { 1755 | "cell_type": "code", 1756 | "metadata": { 1757 | "id": "-0J1xg5WEr4i" 1758 | }, 1759 | "source": [ 1760 | "#!touch run.sh" 1761 | ], 1762 | "execution_count": 8, 1763 | "outputs": [] 1764 | }, 1765 | { 1766 | "cell_type": "markdown", 1767 | "metadata": { 1768 | "id": "9TYiLiKaHn85" 1769 | }, 1770 | "source": [ 1771 | "⚠️ 手动写入八次模拟的指令到新建的run.sh 文件中，为了防止运行模拟中崩溃导致文件结果丢失，在模拟到第五步之前往谷歌云盘备份了一次，最后又全部备份一次，覆盖之前的一次。\n", 1772 | "\n", 1773 | "\n", 1774 | "```\n", 1775 | "export PATH=/content/NAMD_3.0alpha8_Linux-x86_64-netlrts-smp-CUDA:$PATH &&\n", 1776 | "cd /content/1MQ5/eABF/001_RMSD_bound &&\n", 1777 | "namd3 +p2 abf.conf > 001.log $$\n", 1778 | "cd /content/1MQ5/eABF/002_euler_theta &&\n", 1779 | "namd3 +p2 abf.conf > 002.log &&\n", 1780 | "cd /content/1MQ5/eABF/003_euler_phi &&\n", 1781 | "namd3 +p2 abf.conf > 003.log &&\n", 1782 | "cd /content/1MQ5/eABF/004_euler_psi &&\n", 1783 | "namd3 +p2 abf.conf > 004.log &&\n", 1784 | "#中间备份一下，先把已经完成的四个模拟复制到云盘\n", 1785 | "cp -r /content/1MQ5 /content/drive/MyDrive/Colab谷歌计算平台50美元算力测试 &&\n", 1786 | "cd /content/1MQ5/eABF/005_polar_theta &&\n", 1787 | "namd3 +p2 abf.conf > 005.log &&\n", 1788 | "cd /content/1MQ5/eABF/006_polar_phi &&\n", 1789 | "namd3 +p2 abf.conf > 006.log &&\n", 1790 | "cd /content/1MQ5/eABF/007_r &&\n", 1791 | "namd3 +p2 abf.conf > 007.log &&\n", 1792 | "cd /content/1MQ5/eABF/008_RMSD_unbound &&\n", 1793 | "namd3 +p2 abf.conf > 008.log\n", 1794 | "\n", 1795 | "cp -r /content/1MQ5 /content/drive/MyDrive/Colab谷歌计算平台50美元算力测试\n", 1796 | "```\n", 1797 | "\n" 1798 | ] 1799 | }, 1800 | { 1801 | "cell_type": "code", 1802 | "metadata": { 1803 | "colab": { 1804 | "base_uri": "https://localhost:8080/" 1805 | }, 1806 | "id": "nE9HmZdzGa1u", 1807 | "outputId": "a6f911cd-0d96-492c-cf16-4701ba762bf1" 1808 | }, 1809 | "source": [ 1810 | "#!bash run.sh" 1811 | ], 1812 | "execution_count": null, 1813 | "outputs": [ 1814 | { 1815 | "output_type": "stream", 1816 | "name": "stdout", 1817 | "text": [ 1818 | "FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CLGR1 LPH (ATOMS 3709 3656)\n", 1819 | "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT\n" 1820 | ] 1821 | } 1822 | ] 1823 | }, 1824 | { 1825 | "cell_type": "markdown", 1826 | "metadata": { 1827 | "id": "u9rMR7AtqB9a" 1828 | }, 1829 | "source": [ 1830 | "**重命名READMNE，准备提交任务**" 1831 | ] 1832 | }, 1833 | { 1834 | "cell_type": "code", 1835 | "metadata": { 1836 | "id": "94BAplrzp-g4" 1837 | }, 1838 | "source": [ 1839 | "!cat README > run.csh" 1840 | ], 1841 | "execution_count": 9, 1842 | "outputs": [] 1843 | }, 1844 | { 1845 | "cell_type": "markdown", 1846 | "metadata": { 1847 | "id": "hkiMFvmbGfu-" 1848 | }, 1849 | "source": [ 1850 | "**手动修改run.csh中的namd3的路径；并在最后添加将模拟结果复制到谷歌云盘的命令**" 1851 | ] 1852 | }, 1853 | { 1854 | "cell_type": "code", 1855 | "metadata": { 1856 | "colab": { 1857 | "background_save": true 1858 | }, 1859 | "id": "iIQsYdo_c7K3" 1860 | }, 1861 | "source": [ 1862 | "!csh run.csh" 1863 | ], 1864 | "execution_count": null, 1865 | "outputs": [] 1866 | }, 1867 | { 1868 | "cell_type": "markdown", 1869 | "metadata": { 1870 | "id": "_yvl_tnEtRpq" 1871 | }, 1872 | "source": [ 1873 | "**待完成后，将结果拷贝到谷歌云盘drive**" 1874 | ] 1875 | }, 1876 | { 1877 | "cell_type": "code", 1878 | "metadata": { 1879 | "id": "HqGupLA8tF9q" 1880 | }, 1881 | "source": [ 1882 | "#%cd /content" 1883 | ], 1884 | "execution_count": null, 1885 | "outputs": [] 1886 | }, 1887 | { 1888 | "cell_type": "code", 1889 | "metadata": { 1890 | "id": "Ty6-_lootP3O" 1891 | }, 1892 | "source": [ 1893 | "#!tar -cvf 1mq5_10ns.tar.gz charmm-gui-3159213244" 1894 | ], 1895 | "execution_count": null, 1896 | "outputs": [] 1897 | }, 1898 | { 1899 | "cell_type": "code", 1900 | "metadata": { 1901 | "id": "pEjSILzCtimX" 1902 | }, 1903 | "source": [ 1904 | "#!cp 1mq5_10ns.tar.gz /content/drive/MyDrive/Colab谷歌计算平台50美元算力测试" 1905 | ], 1906 | "execution_count": null, 1907 | "outputs": [] 1908 | } 1909 | ] 1910 | } --------------------------------------------------------------------------------