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

Fri Apr 1 15:20:10 CEST 2016

On 4/1/16 4:31 AM, bio hpc wrote:
> Did anybody of you wrote such script or can that be found in some repository?
>

The specifics depend on the input file itself, and different programs write 
different names (an unfortunate truth that not everyone sticks to IUPAC/IUPAB 
nomenclature), and sometimes force fields have their own quirks.  It's just a 
listing of sed commands based on each residue.  But the easiest way has already 
been suggested: use -ignh and specify protonation states when running pdb2gmx. 
The initial H coordinates themselves are going to change as soon as you run 
energy minimization, so preserving these exact coordinates has no bearing on 
anything of importance.  Key interactions will be preserved only if the force 
field represents them correctly, which is another issue entirely.

-Justin

>> 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.
>>>> --
>>>> 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
>>
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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

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