[gmx-users] pulling simulation

[Justin Lemkul]

On 7/9/16 1:44 AM, Hassan Aaryapour wrote:
> Dear Justin A. Lemkul,
>
> Thank you for answer. In US simulation the initial configurations were
> generated by translating ligand along the z-axis up to desired distance. Is
> it necessary to rotate my protein complex in correct orientation until
> protein exit side align with the z-axis and ligand could leave its binding

No alignment is necessary.

> site? How can I find exit site in protein? The binding pocket is deeply
> buried inside the protein and not solvent accessible.
>

If there are multiple paths and nothing is known about the interactions, you 
would have to sample all of them.  Usually the path is apparent, though.  A deep 
channel is good news, because that means the reaction coordinate should be very 
easy to determine.

-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

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