关于锌酶力场选择的求助

tianfu1899 · 发表于 Post on 2021-7-20 01:03:19

样品是小肽，用vina对接蛋白（含有锌）后，导出复合物，然后用gmx做md，gmx pdb2gmx时，出现报错“Fatal error:The residues in the chain ASP40--ZN701 do not have a consistent type. The first residue has type 'Protein', while residue ZN701 is of type 'Ion'. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory. If there are other molecules such as ligands, they should not have the same chain ID as the adjacent protein chain since it's a separate molecule.” 把复合物中的锌去掉过后，可以正常加力场。请问这种情况应该怎么解决？谢谢。刚刚接触这一块，很多地方不是很了解，希望各位老师帮帮忙，谢谢

sobereva · 发表于 Post on 2021-7-20 01:52:16

pdb有问题。没你的pdb不好说
可以把Zn放在pdb最后并作为HETATM字段（参考RCSB上带金属离子的pdb文件）。不要让Zn和蛋白质部分有共同的Chain编号

tianfu1899 · 发表于 Post on 2021-7-20 16:15:03

sobereva 发表于 2021-7-20 01:52
pdb有问题。没你的pdb不好说
可以把Zn放在pdb最后并作为HETATM字段（参考RCSB上带金属离子的pdb文件）。不 ...

sob老师，我重新弄了一下，还是报错：The residues in the chain ASP40--ZN701 do not have a consistent type. The first residue has type 'Protein', while residue AMN0 is of type 'Other'.Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory. If there are other molecules such as ligands, they should not have the same chain ID as the adjacent protein chain since it's a separatemolecule." 麻烦你看看一下pdb文件，谢谢

complex_2spdbv.pdb (343.05 KB, 下载次数 Times of downloads: 22)

sobereva · 发表于 Post on 2021-7-20 18:29:04

把链名改了
HETATM 4699 ZN ZN A 701 43.821 38.240 46.712 1.00 25.11

tianfu1899 · 发表于 Post on 2021-7-20 19:03:08

sobereva 发表于 2021-7-20 18:29
把链名改了
HETATM 4699 ZN ZN A 701 43.821 38.240 46.712 1.00 25.11

你好，sob老师，改了，但是还是报错：The residues in the chain ASP40--CXL3 do not have a consistent type. The first
residue has type 'Protein', while residue AMN0 is of type 'Other'. Either
there is a mistake in your chain, or it includes nonstandard residue names
that have not yet been added to the residuetypes.dat file in the GROMACS
library directory. If there are other molecules such as ligands, they should
not have the same chain ID as the adjacent protein chain since it's a separate
molecule.“出现这种情况过后，我在蛋白的最后一个位置下面加了一个TER, 就是把蛋白和我的小肽，分开。但是还是报错“Fatal error:
The residues in the chain AMN0--CXL3 do not have a consistent type. The first
residue has type 'Other', while residue CYS1 is of type 'Protein'. Either
there is a mistake in your chain, or it includes nonstandard residue names
that have not yet been added to the residuetypes.dat file in the GROMACS
library directory. If there are other molecules such as ligands, they should
not have the same chain ID as the adjacent protein chain since it's a separate
molecule.“ 请问一下，这种情况怎么改呢？谢谢

sobereva · 发表于 Post on 2021-7-20 21:27:45

tianfu1899 发表于 2021-7-20 19:03
你好，sob老师，改了，但是还是报错：The residues in the chain ASP40--CXL3 do not have a consistent ...

CXL3这种非蛋白质的残基也不要和蛋白质有相同的链号

tianfu1899 · 发表于 Post on 2021-7-20 23:06:37

sobereva 发表于 2021-7-20 21:27
CXL3这种非蛋白质的残基也不要和蛋白质有相同的链号

sob老师，全部改了，还是报错：Fatal error:
Residue 'AMN' not found in residue topology database“请问一下，这种这么解决呢！谢谢

sobereva · 发表于 Post on 2021-7-21 02:43:48

tianfu1899 发表于 2021-7-20 23:06
sob老师，全部改了，还是报错：Fatal error:
Residue 'AMN' not found in residue topology database“ ...

rtp文件里没有AMN的定义，自己想办法加上

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[GROMACS] 关于锌酶力场选择的求助

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