[gmx-users] protein-ligand simmulation
r.amandeep2677 at gmail.com
Fri Apr 28 08:51:21 CEST 2017
now it is working my further concern is to put my ligand in its native
location and then simulate
so can you please tell me how to simulate ligand in a particular site of
On Wed, Apr 26, 2017 at 7:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 4/26/17 9:22 AM, Aman Deep wrote:
>> I am trying to simulate protein-ligand complex simulation and I have
>> followed the tutorial of Bevan lab but in energy minimization step it
>> me this error...
>> *Fatal error:*
>> *Atom type CH1 not found*
>> *For more information and tips for troubleshooting, please check the
>> I have made drug.itp file from prodrug and include it in topol.top file
>> still it is giving me the error...
> Likely you're trying to mix and match force fields, as CH1 is a valid type
> for any GROMOS parameter set.
> But don't use PRODRG; as the tutorial warns (and as I am on record a
> million times over saying) the quality of those topologies is inadequate
> for MD simulations. You'll have to correct it significantly or use a
> better source of parameters (manual reparametrization, ATB server, etc).
> 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
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