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标题: Why i get a fatal error in Gromacs using the command pdb2gmx ? [打印本页]

作者
Author: maximos 时间: 2021-2-23 07:37
标题: Why i get a fatal error in Gromacs using the command pdb2gmx ?
Hi, How is it going everybody,
It's my first time trying to perform an MD Simulation using Gromacs, for that, i used a protein already used for a docking study (prepared in ADTtools by removing water molecules and adding charges),
but when i run the command gmx pdb2gmx -f protein.pdb -o protein.gro -p protein.top -water spce, i get an error (please see screenshot).
I attached the protein.pdb files and a text file with all the informations.

Many thanks in advance,
Maximos

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作者
Author: sobereva 时间: 2021-2-23 09:50
Add "-ignh" and retry.
This is because name of some hydrogens in pdb file is not consistent with standard naming.

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