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

[sun]

I think using -ignh does not "remove" hydrogens. Hence, you can use it.

Sent from my iPhone

> On 30-Mar-2016, at 6:04 pm, rajendra kumar <rjdkmr at gmail.com> wrote:
> 
> 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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