[gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?

[Victor Ma]

Thanks James and Justin!
My target is a big membrane protein. So far i've been using charmm-gui to
set up my simulations. And for the movie, I need to keep the lipids. So
with a charmm-gui pre-setup, can I still implement the "pull code" easily?

Thanks!!!

Victor

On Wed, Aug 26, 2015 at 10:51 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/26/15 1:47 PM, Barnett, James W wrote:
>
>> Look into the pull code. You'll want to choose two groups (one for the
>> ligand, one for the binding site), and one coordinate with those groups
>> where the pull rate is not zero (negative rate to bring them together,
>> positive rate to pull them apart).
>>
>>
> And if the purpose is just some cute movie that is not necessarily
> scientifically relevant (shakes head sadly), restrain the protein in some
> way to avoid the inherent problem of "hitting a moving target."
>
> -Justin
>
>
> --
>> James “Wes” Barnett, Ph.D. Candidate
>> Louisiana Board of Regents Fellow
>> Chemical and Biomolecular Engineering
>>
>> Tulane University
>> 341-B Lindy Boggs Center for Energy and Biotechnology
>> 6823 St. Charles Ave
>> New Orleans, Louisiana 70118-5674
>> jbarnet4 at tulane.edu
>>
>>
>> ________________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Victor
>> Ma <victordsmagift at gmail.com>
>> Sent: Wednesday, August 26, 2015 12:31 PM
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] what's the easiest way to generate a md trajectory
>> for ligand flying into/being pulled out of the pocket?
>>
>> hello all
>>
>> I got a urgent request to make a MD movie for pulling the ligand out of
>> the
>> binding site/or the ligand flying into the pocket . I feel like i need to
>> run something like steered md, which I've never done before. So can anyone
>> please suggest a quick and "dirty" way to generate such a movie?
>>
>> Thank you!!
>>
>> Victor
>> --
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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
>
> ==================================================
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