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标题: gromacs生成蛋白质拓扑时氢原子异常的问题 [打印本页]

作者
Author:
yuguang    时间: 2025-5-15 19:15
标题: gromacs生成蛋白质拓扑时氢原子异常的问题
vina对接,得到蛋白质配体复合物之后,把蛋白质和配体抠出来分别制作拓扑文件,但是制作蛋白质的拓扑文件时会发生以下报错:Fatal error:
Atom HN3 in residue ASN 2 was not found in rtp entry ASN with 16 atoms
while sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
若使用对接前的蛋白质制作拓扑,则复合物中蛋白质和配体会相隔很远,溶剂化时需要大量溶剂,后续计算根本算不动。

作者
Author:
sobereva    时间: 2025-5-15 20:58
pdb2gmx带上-ignh
作者
Author:
13277552957    时间: 2025-5-15 21:34
命令加上-ignh,或者用pymol去掉所有氢
作者
Author:
yuguang    时间: 2025-5-16 10:30
感谢老师回答,我加上了-ignh后成功输出了拓扑文件,但在溶剂化时会出现蛋白和配体相隔甚远,导致需要大量溶剂,体系过大无法进行能量最小化,请怎这种问题该怎么解决,绿色为蛋白质,最右面红色为配体
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