多肽模拟时gromos54A7力场的问题

不去重蹈

大家好，我有一个关于gromacs力场的问题。我在用gromacs算多肽的时候，用的是gromos54A7力场，在用pdb2gmx生成拓扑文件时，每一条肽链都有两个warning。一个是针对肽链第一个的残基的H氢原子，一个是争对肽链最后一个残基的O原子。用AMBER99SB-ILDN protein力场就没有warning。以CCY为例采用VMD建模和gaussview，建模都出现同样的问题。换用其他序列也会出现同样的问题，希望大家有时间可以帮忙解答一下，非常感谢。
WARNING: WARNING: Residue 1 named CYS of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.

WARNING: WARNING: Residue 3 named TYR of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.

sobereva

把pdb2gmx的具体运行命令贴出来

不去重蹈

sobereva 发表于 2021-10-17 05:59
把pdb2gmx的具体运行命令贴出来

Command line:
  gmx pdb2gmx -f .\CCY.pdb -o .\CCY.gro -p topol.top -ignh


Select the Force Field:
From 'D:/simulation-tool/gmx2019.3_GPU/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-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
9: CHARMM36 all-atom force field (March 2019)
10: clay
11: GROMOS96 43a1 force field
12: GROMOS96 43a2 force field (improved alkane dihedrals)
13: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
14: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
16: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
17: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
16

Using the Gromos54a7 force field in directory gromos54a7.ff

Opening force field file D:\simulation-tool\gmx2019.3_GPU/share/gromacs/top/gromos54a7.ff/watermodels.dat

Select the Water Model:
1: SPC    simple point charge, recommended
2: SPC/E  extended simple point charge
3: None
2
going to rename gromos54a7.ff/aminoacids.r2b
Opening force field file D:\simulation-tool\gmx2019.3_GPU/share/gromacs/top/gromos54a7.ff/aminoacids.r2b
Reading .\CCY.pdb...
Read '', 25 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 25 atoms

  chain  #res #atoms
  1 'A'     3     25

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file D:\simulation-tool\gmx2019.3_GPU/share/gromacs/top/gromos54a7.ff/atomtypes.atp
Atomtype 59
Reading residue database... (Gromos54a7)
Opening force field file D:\simulation-tool\gmx2019.3_GPU/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper dihedral
Residue 108
Sorting it all out...
Opening force field file D:\simulation-tool\gmx2019.3_GPU/share/gromacs/top/gromos54a7.ff/aminoacids.hdb
Opening force field file D:\simulation-tool\gmx2019.3_GPU/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
Opening force field file D:\simulation-tool\gmx2019.3_GPU/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb
Processing chain 1 'A' (25 atoms, 3 residues)
Identified residue CYS1 as a starting terminus.
Identified residue TYR3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                    CYS1
                     SG6
    CYS2    SG12   0.664
Start terminus CYS-1: NH3+
End terminus TYR-3: COO-
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 3 residues with 37 atoms
Making bonds...
Number of bonds was 42, now 37
Generating angles, dihedrals and pairs...

WARNING: WARNING: Residue 1 named CYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 3 named TYR of a molecule in the input file was mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.


Before cleaning: 46 pairs
Before cleaning: 75 dihedrals
Making cmap torsions...
There are   20 dihedrals,   20 impropers,   54 angles
            46 pairs,       37 bonds and     0 virtual sites
Total mass 387.470 a.m.u.
Total charge 0.000 e
Writing topology

sobereva

不用管这俩warning，对末端残基总会出现，因为氮端残基没有名字叫H的原子（肽键的氢）、碳端残基没有名字叫O的原子（肽键的氧）。