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在24年参加了sob社长的分子动力学与gromacs培训班受益匪浅，回来以后尝试计算蛋白与聚合物分子的相互作用。但是由于该聚合物分子没有现成的力场参数，因此在多方、多次向sob老师请教后，成功用g16配合multiwfn和Sobtop分别计算出该聚合物前端，重复单元，和尾端的RESP电荷并获得.rtp文件。
聚合物分子式如下(n=16)：
为了应用gmx pdb2gmx拼接该聚合物的力场参数，经过学习Gromacs非标准残基的拓扑建立：基于amber力场 - 知乎该贴，对.rtp文件进行处理并放入amber99SB.ff目录，并在residuetypes.dat中添加三个残基的名称，前端CCB，重复单元CB，尾部NCB，定义成protein。并将gro文件与rtp文件进行对应修改，便于pdb2gmx识别。
结果出现一下报错：
GROMACS: gmx pdb2gmx, version 2018.8
Executable: C:\gmx2018.8\bin\gmx.exe
Data prefix: C:\gmx2018.8
Working dir: C:\gmx2018.8\bin
Command line:
gmx pdb2gmx -f z21.gro
Select the Force Field:
From 'C:/gmx2018.8/share/gromacs/top':
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6
Using the Amber99sb_LIPID force field in directory amber99sb_LIPID.ff
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff\watermodels.dat
Select the Water Model:
1: TIP3P TIP 3-point, recommended
2: TIP4P TIP 4-point
3: TIP4P-Ew TIP 4-point optimized with Ewald, recommended
4: TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
5: SPC simple point charge
6: SPC/E extended simple point charge
7: None
1
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/aminoacids.r2b
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/dna.r2b
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/rna.r2b
Reading z21.gro...
Read 'z21', 221 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 3 residues with 221 atoms
chain #res #atoms
1 ' ' 3 221
No occupancies in z21.gro
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/atomtypes.atp
Atomtype 67
Reading residue database... (amber99sb_LIPID)
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/CB.rtp
Residue 1
Sorting it all out...
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/CCB.rtp
Residue 2
Sorting it all out...
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/NCB.rtp
Residue 3
Sorting it all out...
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/aminoacids.rtp
Residue 95
Sorting it all out...
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/dna.rtp
Residue 111
Sorting it all out...
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/rna.rtp
Residue 127
Sorting it all out...
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/aminoacids.hdb
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/dna.hdb
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/rna.hdb
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/aminoacids.n.tdb
Opening force field file C:\gmx2018.8/share/gromacs/top/amber99sb_LIPID.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 (221 atoms, 3 residues)
Identified residue CCB1 as a starting terminus.
Identified residue NCB3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program: gmx pdb2gmx, version 2018.8
Source file: src\gromacs\gmxpreprocess\pdb2top.cpp (line 1096)
Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal residues
so that they match the residue database (.rtp) entries, or provide terminal
database entries (.tdb).
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
.rtp文件和.gro文件附在后面了，其中.gro目前只包含一个单体，先进行尝试，但实际聚合物有16个重复单元，解决报错以后拼接。
CB.rtp
(25.17 KB, 下载次数 Times of downloads: 4)
CCB.rtp
(89.97 KB, 下载次数 Times of downloads: 4)
NCB.rtp
(23.68 KB, 下载次数 Times of downloads: 3)
residuetypes.dat
(2.67 KB, 下载次数 Times of downloads: 3)
z21.gro
(9.99 KB, 下载次数 Times of downloads: 5)
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发表于 Post on 2025-3-4 00:28:12
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