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

[gozde ergin]

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.

> 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
> 
> -- 
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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