标题: pdb2gmx命令报错Residue 'TFE' not found in residue topology database [打印本页] 作者Author: kk5511 时间: 2025-6-26 23:36 标题: pdb2gmx命令报错Residue 'TFE' not found in residue topology database 本帖最后由 kk5511 于 2025-6-26 23:57 编辑
各位前辈好，我先用packmol建好了溶剂盒子，然后尝试用pdb2gmx命令时报错：
Fatal error:
Residue 'TFE' not found in residue topology database
我使用的是amber03力场，结构中含B元素，所以在atomtypes.atp中添加了一行：
B 10.81100
在ffbonded.itp中添加了几个键和角参数：
[ bondtypes ]
; i j func b0 kb
B OS 1 0.14744 235299.1 ; added at 20250626
[ angletypes ]
; i j k func th0 cth
OS B OS 1 110.543 217.977 ; added at 20250626
B OS CT 1 118.002 589.152 ; added at 20250626
[ dihedraltypes ]
;i j k l func
B OS CT CT 9 0.000 1.60387 3 ; added at 20250626
B OS CT H1 9 0.000 1.60387 3 ; added at 20250626
Os B OS CT 9 0.000 0.00000 1 ; added at 20250626
然后看到其他帖子提到rtp中缺少对应的残基，所以在对应力场目录下的aminoacids.rtp添加了相应的结构，包含了atoms和bands两项：
[ TFE ]
[ atoms ]
B BC 0.925055 1
……
[ bonds ]
B O1
……
Using the Amber03 force field in directory amber03.ff
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/watermodels.dat
going to rename amber03.ff/aminoacids.r2b
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/aminoacids.r2b
going to rename amber03.ff/dna.r2b
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/dna.r2b
going to rename amber03.ff/rna.r2b
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/rna.r2b
Reading solution.pdb...
Read 'Built with Packmol', 1860 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 820 residues with 1860 atoms
chain #res #atoms
1 'A' 20 660
2 'B' 800 1200
All occupancies are one
All occupancies are one
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/atomtypes.atp
Reading residue database... (Amber03)
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/aminoacids.rtp
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/dna.rtp
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/rna.rtp
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/aminoacids.hdb
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/dna.hdb
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/rna.hdb
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/aminoacids.n.tdb
Opening force field file /public/software/apps/gromacs/2023/2023.2/share/gromacs/top/amber03.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.13#
Processing chain 1 'A' (660 atoms, 20 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
Fatal error:
Residue 'TFE' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1作者Author: sobereva 时间: 2025-6-27 03:59