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

[rajendra kumar]

Hi,

As suggested above, use -ignh to ignore hydrogen atoms. To use a specific
Histidine, you may change residue name HIS to HIP(Amber)/HSP(Charmm)/HISH(
​OPLS​
) or HID(Amber)/HSD(Charmm)/HISD(
​OPLS​
) or HIE(Amber)/HSE(Charmm)/HISE(
​OPLS​
) either in PDB file or interactively through pdb2gmx usng -his command.


On Wed, Mar 30, 2016 at 12:27 PM, 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,
> BIO-HPC
>
>
>
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