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

[Justin Lemkul]

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.
>> --
>> Gromacs Users mailing list
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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.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================