[gmx-users] protein-ligand simmulation

[Aman Deep]

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
protein.?

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
>> gives
>> me this error...
>>
>> *Fatal error:*
>> *Atom type CH1 not found*
>> *For more information and tips for troubleshooting, please check the
>> GROMACS*
>>
>> I have made drug.itp file from prodrug and include it in topol.top file
>> but
>> 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
>
> --
> ==================================================
>
> 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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-- 
Aman Deep
MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025