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

[Justin Lemkul]

On 8/26/15 1:55 PM, Victor Ma wrote:
> 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?
>

The advice given does not depend on whether or not there are lipids.  It's very 
simple to position the ligand in some straight line along which you pull it.

-Justin

> 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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
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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

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