[gmx-users] pulling simulation

[Hassan Aaryapour]

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

Best Wishes
Hassan



On Tue, Jul 5, 2016 at 5:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/5/16 3:30 AM, Hassan Aaryapour wrote:
>
>> Dear Justin A. Lemkul,
>>
>>
>>
>> How do you calculated the coordinates for center (3.280, 2.181, 2.4775)
>> and
>> box dimensions 6.560 x 4.362 x 12 in Umbrella Sampling by the following
>> program:
>>
>> gmx editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
>> 6.560 4.362 12.
>>
>>
> I defined an original box that was 1 nm larger than any protein atom in
> all 3 dimensions, and then took x/2, y/2, and sufficient space along z to
> pull as far as I needed to.
>
> When I calculate the geometrical center by chimera or accelrys discover
>> studio for my protein complex, it was emerged from box edges. How to
>> resolve it by softwares (not manually)?
>>
>>
> I don't know what magic capabilities each program has, though there's no
> reason to do any of it outside of GROMACS.  The solution is
> system-specific, so I don't know that you can really get away from having
> to do something manually.  The initial box definition is done with editconf
> -d (automatic) but then the actual box vectors needed depend on the size of
> the proteins and the length of the reaction coordinate (something that
> needs to be set by the user).
>
> -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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