pdb2gmx报错Warning: No residues in chain starting at HEM142 identified as Pro...

ZXFroy

[新人求助]求助pdb2gmx运行报错，想知道这个残基怎么补充完整


Warning: No residues in chain starting at HEM142 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.

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
Special Atom Distance matrix:
                  HEM142  HEM142
                   CAB20   CAC27
  HEM142   CAC27   0.799
  HEM142    FE43   0.571   0.573

sobereva

HEM Protein加入residuetypes.dat再试

ZXFroy

sobereva 发表于 2022-11-16 19:50
HEM Protein加入residuetypes.dat再试

sob老师，我把HEM Protein加入residuetype.dat之后有新的报错
Fatal error:
Residue 'HEM' not found in residue topology database是还需要在其他某个文件里面加东西吗

sobereva

ZXFroy 发表于 2022-11-21 11:36
sob老师，我把HEM Protein加入residuetype.dat之后有新的报错
Fatal error:
Residue 'HEM' not found i ...

pdb里所有残基名在rtp文件里必须有定义才能用pdb2gmx，搞清楚pdb2gmx基本运行原理