[gmx-users] Use pdb file generated with Maestro, in Gromacs

SAKO MIRZAIE sako.biochem at gmail.com
Wed Mar 30 13:57:06 CEST 2016

use -ignh flag in pdb2gmx, or you can use of "swiss pdbviewer"
software to correct your pdb.

On 3/30/16, bio hpc <biohpc2015 at gmail.com> wrote:
> Hi,
> we have created some protein pdb files with Maestro. When we try to un an MD
> simulation with gromacs, we get errors like:
>>> Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14 atoms
> I tried to find a solution and it seems that internal gromacs dictionary for
> hydrogens is different from the one from Maestro and other formats. It
> seems, from what I read, that one must convert all hydrogen types to Gromacs
> format. Is is there any script that can do this automatically?
> Of course, there is the option “ignore hydrogens”, but this would be bad for
> us, since we need some histidines in the binding site, and so on.
> Thanks,
> --
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sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj, Iran





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