[gmx-users] ligand-protein simulation

[xiao]

Hi Justin,
 
Thank you very much for your response.
I used GAFF force field parameters for the ligand. I have done another short MD simulation, and this time everything seems fine, so i have no idea where the problem is from.
 
Best wishes
Fugui




At 2013-11-01 20:41:46,"Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 11/1/13 5:37 AM, xiao wrote:
>> Dear all gromacs users,
>>
>> I have run a protein-ligand simulations. However, the position of the ligand
>> is not reasonable after 10ns simulation. There is no problem with the force
>> field paramers of the ligand. I am trying to constrict the ligand move for
>> 500ps simulation. But i do not know whether it will work. Any good idea is
>> appreciated :)
>>
>
>Usually when something misbehaves, the topology is the first likely source of 
>error.  How have you concluded that it is suitable?
>
>Since we don't know what you're doing (description of your protocol, or even 
>better, .mdp files), it could simply be that you're doing something that causes 
>the physical model to be wrong.  Provide that information and you're more likely 
>to get a quick and productive response.
>
>-Justin
>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 601
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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