[gmx-users] CHARMM-GUI files give error in Gromacs

[Justin Lemkul]

On 9/2/16 10:43 AM, gozde ergin wrote:
> Ok I understand. I did exactly same thing for another molecule (SDS) and everything is working without any error.
> But I do not know what should I do with cis-pinonic.
>

If you upload a tarball of all the GROMACS files provided by CHARMM-GUI, I will 
take a quick look.

-Justin

>> On 02 Sep 2016, at 16:40, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> On 9/2/16 10:39 AM, gozde ergin wrote:
>>> Hi Justin,
>>>
>>> I try to use the CHARMM-GUI files directly. My purpose is simulating the water and ci-pinonic system. Cis-pionic molecules will stay on the water surface and I would like to estimate surface tension reduction.
>>>
>>> What should I change in CHARMM-GUI files?
>>
>> Nothing.  That's my point.  When the system is constructed, CHARMM-GUI builds a PSF and list of force field parameters that it needs.  This information is then converted to GROMACS format.  CHARMM-GUI does an energy evaluation to confirm that everything is present.  That's why it's a bit mystifying that GROMACS fails; by definition, the system, topology, and force field have already been checked for integrity.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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

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