pdb2gmx命令报错Residue 'TFE' not found in residue topology database

kk5511

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  
……

但是现在一直没法解决问题，是我哪里还没想到或者设置的不对吗？请前辈指点

kk5511

Command line:
  gmx_mpi pdb2gmx -f solution.pdb -o solution.gro -ff amber03

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

Select the Water Model:

1: TIP3P     TIP 3-point, recommended

2: TIP4P     TIP 4-point

3: TIP4P-Ew  TIP 4-point optimized with Ewald

4: TIP5P     TIP 5-point (see https://gitlab.com/gromacs/gromacs/-/issues/1348 for issues)

5: SPC       simple point charge

6: SPC/E     extended simple point charge

7: None
1

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

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2023.2
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 616)

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
-------------------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1

sobereva

kk5511 发表于 2025-6-27 00:00
Command line:
  gmx_mpi pdb2gmx -f solution.pdb -o solution.gro -ff amber03

有别人回复之前若需要对帖子进行修改、补充，应直接编辑原帖，不要通过回帖进行补充，导致信息零零碎碎，这点在置顶的新社员必读贴里明确说了。

sobereva

rtp文件里加了[ TFE ]但还有这种提示，只可能没弄对力场目录，导致实际载入的rtp文件不是你改的那个

kk5511

sobereva 发表于 2025-6-27 03:59
有别人回复之前若需要对帖子进行修改、补充，应直接编辑原帖，不要通过回帖进行补充，导致信息零零碎碎， ...

好的，sob老师

proszx

残基不识别，需要添加相应参数，这种建模在AMBER下操作更简单