[gmx-users] Protein-Ligand

[Justin Lemkul]

On 5/16/17 1:31 PM, RAHUL SURESH wrote:
> Dear Justin
> Thank you much.
>
> About the term "curved", even am not exactly clear about it. Book by prof
> Pamela states that sentence. As I feel she must be explaining about much
> deformed protein.
>

Well, that's too many unknowns.  If you're worried about a problem that you 
don't understand, there's little I can suggest as a solution.  There are 
proteins that bend, e.g. to remodel membranes or form higher-order structures 
but that seems to be entirely irrelevant to a case of protein-ligand 
dissociation.  Be very sure that it's not a simple PBC issue, and as I suggested 
before, watch the trajectory to see the details of what's happening.

-Justin

>
> On Tue, 16 May 2017 at 7:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/15/17 9:12 AM, RAHUL SURESH wrote:
>>> Dear Users
>>>
>>> I am tryjng to simulate protein ligand complex using charmm36ff for
>> 100ns.
>>> I found the ligand moving away from the protein around 55ns. I don't
>> think
>>> it s a pbc effect. Is there anything I have done wrong or Should I add
>> any
>>> additional commands.?
>>> Await your valuable advice.
>>>
>>
>> Watch the trajectory and see which interactions break first.  Then
>> consider if
>> your ligand topology needs refinement to deal with such interactions or if
>> it's
>> trying to sample some strained conformation that is incompatible with
>> binding
>> (suggesting an internal/dihedral problem).  Compare with available
>> experimental
>> data; some things just have weak affinity.
>>
>>> PS: Will the ligand move out of protein if the protein is over curved
>> after
>>> interaction?
>>>
>>
>> What does "over curved" mean?
>>
>> -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

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