新建
使用开源项目快速制造GROMACS的REST2拓扑文件
wangxy@dp.tech
推荐镜像 :GROMACS:2020.1
推荐机型 :c2_m4_cpu
赞
目录
背景
REST2增强采样方法（Replica Exchange with Solute Tempering 2）是一种用于分子动力学模拟的高效增强采样技术。通过在不同温度下的副本间交换溶质分子，该方法能够提高模拟中的采样效率，从而更准确地研究分子系统的热力学性质和动力学过程。REST2方法的主要优点是不需要预先了解待研究系统的能量景观信息，且计算成本相对较低。因此，它已经在蛋白质折叠、配体结合和溶剂化等领域得到广泛应用。
环境准备
使用这一脚本，需要拥有一个同时安装GROMACS、RDKit的环境。首先下载PyAutoFEP项目，并安装如下仓库：
代码
文本
[1]
! git clone https://github.com/luancarvalhomartins/PyAutoFEP.git
! pip install networkx parmed
! conda install -c conda-forge rdkit mdtraj -y
! cp PyAutoFEP/all_classes.py PyAutoFEP/os_util.py .
Cloning into 'PyAutoFEP'... remote: Enumerating objects: 623, done. remote: Counting objects: 100% (257/257), done. remote: Compressing objects: 100% (96/96), done. remote: Total 623 (delta 182), reused 223 (delta 161), pack-reused 366 Receiving objects: 100% (623/623), 28.75 MiB | 4.91 MiB/s, done. Resolving deltas: 100% (370/370), done. Updating files: 100% (117/117), done. Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple Requirement already satisfied: networkx in /opt/conda/lib/python3.8/site-packages (3.0) Collecting parmed Downloading https://pypi.tuna.tsinghua.edu.cn/packages/5b/48/d94bf10284cac3daaecdeaa856fcdb5def06c5187d8c0431266b8805ff9d/ParmEd-4.2.2.tar.gz (20.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 20.2/20.2 MB 17.4 MB/s eta 0:00:0000:0100:01 Preparing metadata (setup.py) ... done Building wheels for collected packages: parmed Building wheel for parmed (setup.py) ... done Created wheel for parmed: filename=ParmEd-4.2.2-cp38-cp38-linux_x86_64.whl size=19519669 sha256=810eefe9f7476f47b88da7d5a4bdeb9dd4f92b52234b7f5c7c634ffa6597ac6f Stored in directory: /root/.cache/pip/wheels/3d/3d/e9/a2f0cb7015f2cae9c30f11f43bf4e6e62b043e2bda4abd24d8 Successfully built parmed Installing collected packages: parmed Successfully installed parmed-4.2.2 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv Retrieving notices: ...working... /opt/conda/lib/python3.8/site-packages/urllib3/connectionpool.py:1056: InsecureRequestWarning: Unverified HTTPS request is being made to host 'repo.anaconda.com'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#ssl-warnings warnings.warn( /opt/conda/lib/python3.8/site-packages/urllib3/connectionpool.py:1056: InsecureRequestWarning: Unverified HTTPS request is being made to host 'repo.anaconda.com'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#ssl-warnings warnings.warn( /opt/conda/lib/python3.8/site-packages/urllib3/connectionpool.py:1056: InsecureRequestWarning: Unverified HTTPS request is being made to host 'conda.anaconda.org'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#ssl-warnings warnings.warn( done Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 23.5.2 latest version: 23.10.0 Please update conda by running $ conda update -n base -c defaults conda Or to minimize the number of packages updated during conda update use conda install conda=23.10.0 ## Package Plan ## environment location: /opt/conda added / updated specs: - mdtraj - rdkit The following packages will be downloaded: package | build ---------------------------|----------------- astunparse-1.6.3 | pyhd8ed1ab_0 15 KB conda-forge blosc-1.21.5 | h0f2a231_0 48 KB conda-forge c-blosc2-2.11.2 | hb4ffafa_0 325 KB conda-forge hdf5-1.10.6 | h3ffc7dd_1 3.6 MB defaults libgfortran-ng-13.2.0 | h69a702a_0 23 KB conda-forge libgfortran5-13.2.0 | ha4646dd_0 1.4 MB conda-forge libstdcxx-ng-13.2.0 | h7e041cc_2 3.7 MB conda-forge lzo-2.10 | h516909a_1000 314 KB conda-forge mdtraj-1.9.9 | py38h028faf2_0 1.4 MB conda-forge openssl-1.1.1w | hd590300_0 1.9 MB conda-forge pooch-1.8.0 | pyhd8ed1ab_0 51 KB conda-forge py-cpuinfo-9.0.0 | pyhd8ed1ab_0 24 KB conda-forge pytables-3.8.0 | py38h43249b6_2 2.1 MB defaults pyzmq-24.0.1 | py38hfc09fa9_1 482 KB conda-forge rdkit-2022.09.1 | py38h28c1a8d_0 39.9 MB conda-forge scipy-1.10.1 | py38hf6e8229_1 22.4 MB defaults snappy-1.1.10 | h9fff704_0 38 KB conda-forge zlib-ng-2.0.7 | h0b41bf4_0 92 KB conda-forge ------------------------------------------------------------ Total: 77.7 MB The following NEW packages will be INSTALLED: astunparse conda-forge/noarch::astunparse-1.6.3-pyhd8ed1ab_0 blosc conda-forge/linux-64::blosc-1.21.5-h0f2a231_0 c-blosc2 conda-forge/linux-64::c-blosc2-2.11.2-hb4ffafa_0 hdf5 pkgs/main/linux-64::hdf5-1.10.6-h3ffc7dd_1 libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_0 libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-ha4646dd_0 lzo conda-forge/linux-64::lzo-2.10-h516909a_1000 mdtraj conda-forge/linux-64::mdtraj-1.9.9-py38h028faf2_0 pooch conda-forge/noarch::pooch-1.8.0-pyhd8ed1ab_0 py-cpuinfo conda-forge/noarch::py-cpuinfo-9.0.0-pyhd8ed1ab_0 pytables pkgs/main/linux-64::pytables-3.8.0-py38h43249b6_2 scipy pkgs/main/linux-64::scipy-1.10.1-py38hf6e8229_1 snappy conda-forge/linux-64::snappy-1.1.10-h9fff704_0 zlib-ng conda-forge/linux-64::zlib-ng-2.0.7-h0b41bf4_0 The following packages will be UPDATED: ca-certificates pkgs/main::ca-certificates-2023.05.30~ --> conda-forge::ca-certificates-2023.7.22-hbcca054_0 libstdcxx-ng pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_2 openssl pkgs/main::openssl-1.1.1u-h7f8727e_0 --> conda-forge::openssl-1.1.1w-hd590300_0 rdkit 2022.03.2-py38ha829ea6_0 --> 2022.09.1-py38h28c1a8d_0 The following packages will be SUPERSEDED by a higher-priority channel: certifi pkgs/main/linux-64::certifi-2023.7.22~ --> conda-forge/noarch::certifi-2023.7.22-pyhd8ed1ab_0 pyzmq pkgs/main::pyzmq-25.1.0-py38h6a678d5_0 --> conda-forge::pyzmq-24.0.1-py38hfc09fa9_1 Downloading and Extracting Packages pooch-1.8.0 | 51 KB | | 0% libstdcxx-ng-13.2.0 | 3.7 MB | | 0% c-blosc2-2.11.2 | 325 KB | | 0% scipy-1.10.1 | 22.4 MB | | 0% lzo-2.10 | 314 KB | | 0% blosc-1.21.5 | 48 KB | | 0% rdkit-2022.09.1 | 39.9 MB | | 0% py-cpuinfo-9.0.0 | 24 KB | | 0% snappy-1.1.10 | 38 KB | | 0% mdtraj-1.9.9 | 1.4 MB | | 0% openssl-1.1.1w | 1.9 MB | | 0% libgfortran5-13.2.0 | 1.4 MB | | 0% astunparse-1.6.3 | 15 KB | | 0% pytables-3.8.0 | 2.1 MB | | 0% libgfortran-ng-13.2. | 23 KB | | 0% hdf5-1.10.6 | 3.6 MB | | 0% zlib-ng-2.0.7 | 92 KB | | 0% pooch-1.8.0 | 51 KB | ###########5 | 31% libstdcxx-ng-13.2.0 | 3.7 MB | 1 | 0% lzo-2.10 | 314 KB | #8 | 5% c-blosc2-2.11.2 | 325 KB | #8 | 5% pooch-1.8.0 | 51 KB | #######################1 | 63% pooch-1.8.0 | 51 KB | ##################################### | 100% c-blosc2-2.11.2 | 325 KB | #####4 | 15% lzo-2.10 | 314 KB | ################9 | 46% c-blosc2-2.11.2 | 325 KB | ##########9 | 30% lzo-2.10 | 314 KB | ################################ | 87% blosc-1.21.5 | 48 KB | ############4 | 34% libstdcxx-ng-13.2.0 | 3.7 MB | 4 | 1% blosc-1.21.5 | 48 KB | ##################################### | 100% c-blosc2-2.11.2 | 325 KB | ##############5 | 39% lzo-2.10 | 314 KB | ##################################### | 100% libstdcxx-ng-13.2.0 | 3.7 MB | #7 | 5% py-cpuinfo-9.0.0 | 24 KB | ########################2 | 66% py-cpuinfo-9.0.0 | 24 KB | ##################################### | 100% libstdcxx-ng-13.2.0 | 3.7 MB | ##2 | 6% rdkit-2022.09.1 | 39.9 MB | | 0% libstdcxx-ng-13.2.0 | 3.7 MB | ##9 | 8% c-blosc2-2.11.2 | 325 KB | ##################2 | 49% libstdcxx-ng-13.2.0 | 3.7 MB | ###6 | 10% snappy-1.1.10 | 38 KB | ###############5 | 42% snappy-1.1.10 | 38 KB | ##################################### | 100% c-blosc2-2.11.2 | 325 KB | #########################5 | 69% rdkit-2022.09.1 | 39.9 MB | | 0% scipy-1.10.1 | 22.4 MB | | 0% libstdcxx-ng-13.2.0 | 3.7 MB | ####5 | 12% c-blosc2-2.11.2 | 325 KB | ################################8 | 89% c-blosc2-2.11.2 | 325 KB | ##################################### | 100% libstdcxx-ng-13.2.0 | 3.7 MB | #####9 | 16% rdkit-2022.09.1 | 39.9 MB | 5 | 1% scipy-1.10.1 | 22.4 MB | | 0% rdkit-2022.09.1 | 39.9 MB | 8 | 2% scipy-1.10.1 | 22.4 MB | 1 | 0% rdkit-2022.09.1 | 39.9 MB | # | 3% openssl-1.1.1w | 1.9 MB | 3 | 1% rdkit-2022.09.1 | 39.9 MB | #3 | 4% openssl-1.1.1w | 1.9 MB | ##7 | 8% scipy-1.10.1 | 22.4 MB | 2 | 1% libstdcxx-ng-13.2.0 | 3.7 MB | ######9 | 19% rdkit-2022.09.1 | 39.9 MB | #8 | 5% mdtraj-1.9.9 | 1.4 MB | 4 | 1% scipy-1.10.1 | 22.4 MB | 2 | 1% libstdcxx-ng-13.2.0 | 3.7 MB | ########9 | 24% openssl-1.1.1w | 1.9 MB | ####3 | 12% rdkit-2022.09.1 | 39.9 MB | ##4 | 7% libstdcxx-ng-13.2.0 | 3.7 MB | ############6 | 34% openssl-1.1.1w | 1.9 MB | ######8 | 18% rdkit-2022.09.1 | 39.9 MB | ###1 | 8% mdtraj-1.9.9 | 1.4 MB | ##5 | 7% libstdcxx-ng-13.2.0 | 3.7 MB | ########################7 | 67% mdtraj-1.9.9 | 1.4 MB | #######1 | 19% libstdcxx-ng-13.2.0 | 3.7 MB | ##############################7 | 83% scipy-1.10.1 | 22.4 MB | 3 | 1% mdtraj-1.9.9 | 1.4 MB | #########6 | 26% libstdcxx-ng-13.2.0 | 3.7 MB | ##################################### | 100% libstdcxx-ng-13.2.0 | 3.7 MB | ##################################### | 100% scipy-1.10.1 | 22.4 MB | 5 | 1% rdkit-2022.09.1 | 39.9 MB | ###7 | 10% mdtraj-1.9.9 | 1.4 MB | ############1 | 33% openssl-1.1.1w | 1.9 MB | ########9 | 24% rdkit-2022.09.1 | 39.9 MB | ##### | 14% scipy-1.10.1 | 22.4 MB | 7 | 2% mdtraj-1.9.9 | 1.4 MB | ###############4 | 42% openssl-1.1.1w | 1.9 MB | ###########4 | 31% libgfortran5-13.2.0 | 1.4 MB | 4 | 1% scipy-1.10.1 | 22.4 MB | # | 3% rdkit-2022.09.1 | 39.9 MB | ######1 | 17% openssl-1.1.1w | 1.9 MB | ################4 | 44% scipy-1.10.1 | 22.4 MB | #2 | 3% rdkit-2022.09.1 | 39.9 MB | #######1 | 19% openssl-1.1.1w | 1.9 MB | #############################7 | 80% scipy-1.10.1 | 22.4 MB | #5 | 4% rdkit-2022.09.1 | 39.9 MB | ########5 | 23% mdtraj-1.9.9 | 1.4 MB | ################## | 49% openssl-1.1.1w | 1.9 MB | ##################################### | 100% openssl-1.1.1w | 1.9 MB | ##################################### | 100% libgfortran5-13.2.0 | 1.4 MB | #####8 | 16% scipy-1.10.1 | 22.4 MB | #8 | 5% rdkit-2022.09.1 | 39.9 MB | #########5 | 26% mdtraj-1.9.9 | 1.4 MB | #####################7 | 59% scipy-1.10.1 | 22.4 MB | ##1 | 6% rdkit-2022.09.1 | 39.9 MB | ###########3 | 31% astunparse-1.6.3 | 15 KB | ##################################### | 100% astunparse-1.6.3 | 15 KB | ##################################### | 100% mdtraj-1.9.9 | 1.4 MB | ################################2 | 87% libgfortran5-13.2.0 | 1.4 MB | ##################################### | 100% rdkit-2022.09.1 | 39.9 MB | ############4 | 34% libgfortran5-13.2.0 | 1.4 MB | ##################################### | 100% mdtraj-1.9.9 | 1.4 MB | ##################################### | 100% mdtraj-1.9.9 | 1.4 MB | ##################################### | 100% rdkit-2022.09.1 | 39.9 MB | ##############1 | 38% libgfortran-ng-13.2. | 23 KB | ########################## | 70% libgfortran-ng-13.2. | 23 KB | ##################################### | 100% scipy-1.10.1 | 22.4 MB | ##5 | 7% zlib-ng-2.0.7 | 92 KB | ######4 | 17% scipy-1.10.1 | 22.4 MB | ###3 | 9% zlib-ng-2.0.7 | 92 KB | ##################################### | 100% scipy-1.10.1 | 22.4 MB | ####2 | 11% rdkit-2022.09.1 | 39.9 MB | ###############1 | 41% scipy-1.10.1 | 22.4 MB | #####9 | 16% hdf5-1.10.6 | 3.6 MB | 1 | 0% rdkit-2022.09.1 | 39.9 MB | ################8 | 46% pytables-3.8.0 | 2.1 MB | 2 | 1% scipy-1.10.1 | 22.4 MB | #######7 | 21% rdkit-2022.09.1 | 39.9 MB | #################7 | 48% rdkit-2022.09.1 | 39.9 MB | ###################2 | 52% scipy-1.10.1 | 22.4 MB | ########8 | 24% pytables-3.8.0 | 2.1 MB | 5 | 1% pyzmq-24.0.1 | 482 KB | #2 | 3% hdf5-1.10.6 | 3.6 MB | 3 | 1% scipy-1.10.1 | 22.4 MB | ##########7 | 29% rdkit-2022.09.1 | 39.9 MB | ####################3 | 55% scipy-1.10.1 | 22.4 MB | #############2 | 36% rdkit-2022.09.1 | 39.9 MB | #####################4 | 58% hdf5-1.10.6 | 3.6 MB | #2 | 3% pytables-3.8.0 | 2.1 MB | ##4 | 7% rdkit-2022.09.1 | 39.9 MB | ######################6 | 61% rdkit-2022.09.1 | 39.9 MB | #######################6 | 64% pyzmq-24.0.1 | 482 KB | ##################################### | 100% pyzmq-24.0.1 | 482 KB | ##################################### | 100% hdf5-1.10.6 | 3.6 MB | ##2 | 6% scipy-1.10.1 | 22.4 MB | ##############8 | 40% hdf5-1.10.6 | 3.6 MB | ####1 | 11% hdf5-1.10.6 | 3.6 MB | ##### | 14% scipy-1.10.1 | 22.4 MB | ##################3 | 50% hdf5-1.10.6 | 3.6 MB | ######9 | 19% pytables-3.8.0 | 2.1 MB | #####7 | 15% hdf5-1.10.6 | 3.6 MB | ########5 | 23% scipy-1.10.1 | 22.4 MB | ##################### | 57% pytables-3.8.0 | 2.1 MB | ################### | 52% hdf5-1.10.6 | 3.6 MB | ###########2 | 31% rdkit-2022.09.1 | 39.9 MB | ########################7 | 67% pytables-3.8.0 | 2.1 MB | ###################### | 60% rdkit-2022.09.1 | 39.9 MB | ###########################4 | 74% pytables-3.8.0 | 2.1 MB | #############################4 | 80% pytables-3.8.0 | 2.1 MB | ##################################6 | 94% hdf5-1.10.6 | 3.6 MB | ############# | 35% hdf5-1.10.6 | 3.6 MB | ################8 | 46% rdkit-2022.09.1 | 39.9 MB | ############################5 | 77% hdf5-1.10.6 | 3.6 MB | #######################8 | 64% rdkit-2022.09.1 | 39.9 MB | #############################5 | 80% hdf5-1.10.6 | 3.6 MB | #############################2 | 79% scipy-1.10.1 | 22.4 MB | ######################2 | 60% rdkit-2022.09.1 | 39.9 MB | ##############################5 | 83% hdf5-1.10.6 | 3.6 MB | ##################################4 | 93% pytables-3.8.0 | 2.1 MB | ##################################### | 100% rdkit-2022.09.1 | 39.9 MB | ###############################4 | 85% hdf5-1.10.6 | 3.6 MB | ##################################### | 100% scipy-1.10.1 | 22.4 MB | #########################3 | 68% rdkit-2022.09.1 | 39.9 MB | ################################8 | 89% rdkit-2022.09.1 | 39.9 MB | #################################9 | 92% rdkit-2022.09.1 | 39.9 MB | ################################### | 95% scipy-1.10.1 | 22.4 MB | ###########################8 | 75% rdkit-2022.09.1 | 39.9 MB | ####################################1 | 98% scipy-1.10.1 | 22.4 MB | ############################8 | 78% scipy-1.10.1 | 22.4 MB | ###############################3 | 85% scipy-1.10.1 | 22.4 MB | ################################# | 89% scipy-1.10.1 | 22.4 MB | ###################################1 | 95% scipy-1.10.1 | 22.4 MB | ####################################7 | 99% scipy-1.10.1 | 22.4 MB | ##################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done
代码
文本
生成GROMACS拓扑文件，并确保拓扑文件中所有参数都填充数值
代码
文本
[2]
with open("em.mdp", "w") as f:
f.write(""";
; GROMACS
; Energy Minimization Script
;
;
constraints = none
integrator = steep ; steepest decents minimum (else cg)
nsteps = 10000
;
; Energy Minimizing Stuff
;
emtol = 10 ; convergence total force(kJ/mol/nm) is smaller than
emstep = 0.01 ; initial step size (nm)
nstcomm = 100 ; frequency or COM motion removal
ns_type = grid
rlist = 1.4 ; cut-off distance for short range neighbors
rcoulomb = 1.4 ; distance for coulomb cut-off
coulombtype = PME ; electrostatics (Particle Mesh Ewald method)
fourierspacing = 0.12 ; max grid spacing when using PPPM or PME
vdw-type = Cut-off
rvdw = 1.2 ; VDW cut-off
Tcoupl = no ; temperature coupling
Pcoupl = no ; pressure coupling
gen_vel = no""")
! wget https://files.rcsb.org/download/1UBQ.pdb
! gmx pdb2gmx -f 1UBQ.pdb -o clean.gro -p topol.top -ignh -ff amber99sb-ildn -water tip3p -merge all
! gmx editconf -f clean.gro -o box.gro -c -d 1.0 -bt cubic
! gmx solvate -cp box.gro -cs spc216.gro -o solv.gro -p topol.top
! gmx grompp -f em.mdp -c solv.gro -p topol.top -o em.tpr -pp processed.top
import parmed
syst = parmed.gromacs.GromacsTopologyFile("processed.top")
syst.save("processed_cleaned.top")
--2023-11-08 16:15:50-- https://files.rcsb.org/download/1UBQ.pdb Resolving ga.dp.tech (ga.dp.tech)... 10.255.254.37, 10.255.254.7, 10.255.254.18 Connecting to ga.dp.tech (ga.dp.tech)|10.255.254.37|:8118... connected. Proxy request sent, awaiting response... 200 OK Length: unspecified [application/octet-stream] Saving to: ‘1UBQ.pdb’ 1UBQ.pdb [ <=> ] 77.76K 229KB/s in 0.3s 2023-11-08 16:15:51 (229 KB/s) - ‘1UBQ.pdb’ saved [79623] :-) GROMACS - gmx pdb2gmx, 2020.1-Ubuntu-2020.1-1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /data Command line: gmx pdb2gmx -f 1UBQ.pdb -o clean.gro -p topol.top -ignh -ff amber99sb-ildn -water tip3p -merge all Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff going to rename amber99sb-ildn.ff/aminoacids.r2b Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b Reading 1UBQ.pdb... Read 'UBIQUITIN', 660 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 1 blocks of water and 134 residues with 660 atoms chain #res #atoms 1 'A' 76 602 2 ' ' 58 58 (only water) WARNING: there were 0 atoms with zero occupancy and 57 atoms with occupancy unequal to one (out of 660 atoms). Check your pdb file. Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp Reading residue database... (Amber99sb-ildn) Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb Processing chain 1 'A' (602 atoms, 76 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 116 donors and 117 acceptors were found. There are 174 hydrogen bonds Will use HISE for residue 68 Identified residue MET1 as a starting terminus. Identified residue GLY76 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: MET1 SD7 HIS68 NE2540 1.621 WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries WARNING: Duplicate line found in or between hackblock and rtp entries Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 76 residues with 1231 atoms Making bonds... Number of bonds was 1238, now 1237 Generating angles, dihedrals and pairs... Before cleaning: 3273 pairs Before cleaning: 3413 dihedrals Keeping all generated dihedrals Making cmap torsions... There are 3413 dihedrals, 216 impropers, 2257 angles 3264 pairs, 1237 bonds and 0 virtual sites Total mass 8564.922 a.m.u. Total charge 0.000 e Writing topology Processing chain 2 (58 atoms, 58 residues) Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 58 residues with 174 atoms Making bonds... Number of bonds was 116, now 116 Generating angles, dihedrals and pairs... Making cmap torsions... There are 0 dihedrals, 0 impropers, 58 angles 0 pairs, 116 bonds and 0 virtual sites Total mass 1044.928 a.m.u. Total charge 0.000 e Including chain 1 in system: 1231 atoms 76 residues Including chain 2 in system: 174 atoms 58 residues Now there are 1405 atoms and 134 residues Total mass in system 9609.850 a.m.u. Total charge in system 0.000 e Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: 1UBQ.pdb. The Amber99sb-ildn force field and the tip3p water model are used. --------- ETON ESAELP ------------ GROMACS reminds you: "Physics is like sex: sure, it may give some practical results, but that's not why we do it" (Richard P. Feynman) :-) GROMACS - gmx editconf, 2020.1-Ubuntu-2020.1-1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx editconf, version 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /data Command line: gmx editconf -f clean.gro -o box.gro -c -d 1.0 -bt cubic Note that major changes are planned in future for editconf, to improve usability and utility. Read 1405 atoms Volume: 62.9497 nm^3, corresponds to roughly 28300 electrons No velocities found system size : 3.168 3.487 3.857 (nm) diameter : 4.491 (nm) center : 3.025 2.891 1.503 (nm) box vectors : 5.084 4.277 2.895 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 62.95 (nm^3) shift : 0.221 0.355 1.743 (nm) new center : 3.246 3.246 3.246 (nm) new box vectors : 6.491 6.491 6.491 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 273.54 (nm^3) GROMACS reminds you: "There's a limit to how many times you can read how great you are and what an inspiration you are, but I'm not there yet." (Randy Pausch) :-) GROMACS - gmx solvate, 2020.1-Ubuntu-2020.1-1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx solvate, version 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /data Command line: gmx solvate -cp box.gro -cs spc216.gro -o solv.gro -p topol.top Reading solute configuration Reading solvent configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmx solvate uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Generating solvent configuration Will generate new solvent configuration of 4x4x4 boxes Solvent box contains 31230 atoms in 10410 residues Removed 4455 solvent atoms due to solvent-solvent overlap Removed 1359 solvent atoms due to solute-solvent overlap Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 8472 residues Generated solvent containing 25416 atoms in 8472 residues Writing generated configuration to solv.gro Output configuration contains 26821 atoms in 8606 residues Volume : 273.543 (nm^3) Density : 988.617 (g/l) Number of solvent molecules: 8472 Processing topology Adding line for 8472 solvent molecules with resname (SOL) to topology file (topol.top) Back Off! I just backed up topol.top to ./#topol.top.1# GROMACS reminds you: "I have noticed a large, negative correlation between having a well-defined mission workload and concern for the Top500. It's almost like LINPACK is what you focus on when you don't know what to focus on." (Jeff Hammond) :-) GROMACS - gmx grompp, 2020.1-Ubuntu-2020.1-1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /data Command line: gmx grompp -f em.mdp -c solv.gro -p topol.top -o em.tpr -pp processed.top Ignoring obsolete mdp entry 'ns_type' Setting the LD random seed to -1955167258 Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 76 Protein residues There are: 8530 Water residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 54870.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 56x56x56, spacing 0.116 0.116 0.116 Estimate for the relative computational load of the PME mesh part: 0.08 This run will generate roughly 2 Mb of data GROMACS reminds you: "Let us not get carried away with our ideas and take our models too seriously" (Nancy Swanson)
代码
文本
[3]
from all_classes import TopologyData
import numpy as np
from copy import deepcopy
--------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[3], line 1 ----> 1 from all_classes import TopologyData 2 import numpy as np 3 from copy import deepcopy File /data/all_classes.py:29 27 import numpy 28 from collections import OrderedDict ---> 29 import os_util 30 import re 31 from copy import deepcopy File /data/os_util.py:34 31 from ast import literal_eval 32 import time ---> 34 import rdkit.Chem 36 verbosity_level = namedtuple("VerbosityLevel", 37 "error default warning info debug extra_debug timing")(-1, 0, 1, 2, 3, 4, 5) 40 def date_fmt(): File /opt/conda/lib/python3.8/site-packages/rdkit/Chem/__init__.py:23 21 _HasSubstructMatchStr = rdchem._HasSubstructMatchStr 22 from rdkit.Chem.rdchem import * ---> 23 from rdkit.Chem.rdmolfiles import * 24 from rdkit.Chem.rdmolops import * 25 from rdkit.Chem.rdCIPLabeler import * ImportError: /opt/conda/lib/python3.8/site-packages/zmq/backend/cython/../../../../.././libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /opt/conda/lib/python3.8/site-packages/rdkit/Chem/../../../../libRDKitFileParsers.so.1)
代码
文本
[ ]
def set_scale_state(top, scale_factor, scale_indices):
last_atomtype_index = top.output_sequence.index(next(reversed(top.atomtype_dict.values()))) + 1
scale_multiplier = np.sqrt(scale_factor)
atoms = []
for mol in top.molecules:
for atom in mol.atoms_dict.values():
atoms.append(atom)
for s_idx in scale_indices:
atom = atoms[s_idx]
# update charge
atom.q_e = atom.q_e * scale_multiplier
atype_name = atom.atom_type
atype = top.atomtype_dict[atype_name]
# create heat atype
heat_atype = f"{atype_name}_"
if heat_atype not in top.atomtype_dict.keys():
print(f"Add heat atype: {heat_atype}")
heat_atype_data = deepcopy(atype)
heat_atype_data.atom_type = heat_atype
heat_atype_data.q_e = atype.q_e * scale_multiplier
heat_atype_data.W = atype.W * scale_multiplier
heat_atype_data.comments = f'Heated atom type. Original: {atype.V} {atype.W}'
top.atomtype_dict[heat_atype] = heat_atype_data
top.output_sequence.insert(last_atomtype_index, heat_atype_data)
last_atomtype_index += 1
# update LJ
atom.atom_type = heat_atype
print(f"A ({atype_name}) : atype={heat_atype}")
代码
文本
使用MDTraj提取需加热区域的indices
代码
文本
[ ]
# pick all the alpha helix in the protein
import mdtraj as md
gro = md.load("solv.gro")
dssp = md.compute_dssp(gro)
helix = []
for i, ss in enumerate(dssp[0]):
if ss == "H":
helix.append(i)
heat_indices = []
for res in gro.topology.residues:
if res.index in helix:
for atom in res.atoms:
heat_indices.append(atom.index)
代码
文本
放缩被选择部分的分子间相互作用参数。1.0即为不放缩，示例中使用0.5x作为例子。
代码
文本
[ ]
# scale the interaction of selected atoms to 0.5x
scale_factor = 0.5
topdata = TopologyData(topology_files=["processed_cleaned.top"])
set_scale_state(topdata, scale_factor=scale_factor, scale_indices=heat_indices)
with open("heated.top", "w") as f:
f.write(str(topdata))
代码
文本
点个赞吧
推荐阅读
公开
基于Uni-Mol的分子性质预测
Zhifeng Gao
更新于 2024-07-17
7 赞8 转存文件
公开
队伍:T A榜0.7594 Rank4 / B榜0.7759 Rank1
T.T.
发布于 2023-10-31
7 赞9 转存文件
评论
zjgemi