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

[bio hpc]

Thanks. 
Apart from this, is is there some script that keeps my original hydrogens from Maestro?

> El 30/3/2016, a las 19:43, Tsjerk Wassenaar <tsjerkw at gmail.com> escribió:
> 
> Hey :)
> 
> -ignh does ignore the hydrogens in the input file. It builds those
> hydrogens that are specified in the force field. For histidines, the
> protonation state is determined from the possible hydrogen-bonded network,
> but it is possible to assign specific states interactively, using the
> option -his, or by specifying the residue name in the input file.
> 
> Hope it helps,
> 
> Tsjerk
> 
> On Wed, Mar 30, 2016 at 4:42 PM, sun <sun.iba2 at gmail.com> wrote:
> 
>> 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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> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> -- 
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