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

[Victor Ma]

Thank you, Justin! Let me try.

Cheers,
Victor

On Wed, Aug 26, 2015 at 10:57 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

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