[gmx-users] Protein Drug simulation Parameters

[Justin Lemkul]

On 9/27/16 7:32 AM, tasneem kausar wrote:
> Thank you Justin for your reply.
> There is another question regarding MMPBSA energy calculations. I have
> calculated the MMPBSA energy of 8 potential protein+drug complex.
> Simulation time was 50 ns. One of the protein drug complex gives the
> positive binding energy. Does the periodic boundary conditions like whole
> and nojump effect the binding energy.
>

Of course.  You need to provide sensible configurations to analyze.  If the 
trajectory is not imaged properly, the results will be nonsense.  But of course, 
it is simple to tell if the input trajectory is OK - watch it.

-Justin

> On Mon, Sep 26, 2016 at 5:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/26/16 4:43 AM, tasneem kausar wrote:
>>
>>> Dear All
>>>
>>> I have performed MD simulation of protein and drug crystal structure. I
>>> have generated drug  itp file from PRODRG server and corrected the charges
>>> of atoms as suggested in Justin's paper J. Chem. Inf. Model. 2010, 50,
>>> 2221–2235.
>>> I have done 50 ns MD simulation of protein and drug using g43a1 force
>>> field
>>> and spc water model. After 15 ns drug molecule comes out of the pocket.
>>> Is this expected during MD simulation. If this occurs what is the reason
>>> behind it.
>>> Should we change any specific parameter for protein drug simulation.
>>>
>>>
>> First, make sure it is not a simple periodicity issue by re-imaging the
>> trajectory with trjconv.  Several iterations will likely be necessary; see
>> http://www.gromacs.org/Documentation/Terminology/Periodic_
>> Boundary_Conditions#Suggested_trjconv_workflow
>>
>> If there is some legitimate problem that leads to ligand dissociation,
>> either your run settings are inappropriate, the initial geometry has large
>> clashes that lead to large forces that expel the ligand, or the ligand
>> topology is incorrect and overly attracted to the bulk aqueous environment.
>>
>> -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

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