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

[bio hpc]

Did anybody of you wrote such script or can that be found in some repository?

> El 31/3/2016, a las 13:04, Justin Lemkul <jalemkul at vt.edu> escribió:
> 
> 
> 
> On 3/31/16 6:55 AM, bio hpc wrote:
>> Thanks.
>> Apart from this, is is there some script that keeps my original hydrogens from Maestro?
>> 
> 
> Rename with sed according to what the force field expects.
> 
> -Justin
> 
>>> 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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>> 
>> 
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
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> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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