gromacs生成蛋白质拓扑时氢原子异常的问题

yuguang

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。

sobereva

pdb2gmx带上-ignh

13277552957

命令加上-ignh，或者用pymol去掉所有氢

yuguang

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