[gmx-users] Center of mass restraints

[Justin Lemkul]

On 11/11/19 3:58 PM, Daniel Burns wrote:
> Thank you!
>
> If I use the coordinates of the center of mass for the spherical restraint,
> will the ligand remain restrained to that coordinate if the protein rotates
> or translates the binding site away from that original position?

No, that's only possible with the pull code. If you're just trying to do 
a simple pose refinement, you could apply a light restraint on the 
backbone or C-alpha atoms to prevent this from happening.

>   Or am I
> going about this wrong?  Can I set up that spherical restraint with a
> genrestr command without calculating the coordinates of the center of mass
> from a visualization software?

genrestr won't generate what you need.

Obtain the COM coordinates of your desired residues with gmx traj -ox 
-com and a suitable index group. That's the origin of the restraint. 
Create a (physically unrealistic) coordinate file where all the ligand 
atoms are set to those coordinates.

> I haven't been able to find an example of this.

Probably good fodder for my next tutorial...there are lots of practical 
applications to using the flat-bottom restraints.

-Justin

> On Mon, Nov 11, 2019 at 8:25 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 11/10/19 2:54 PM, Daniel Burns wrote:
>>> Hello,
>>>
>>> I have identified a set of amino acid residues that surround a small
>>> molecule binding site.  How would I go about restraining the small
>> molecule
>>> ligand to the center of mass of the surrounding residues?  I want the
>>> molecule to be able to bounce around in the binding site to let if find
>> the
>>> most energetically favorable configuration.
>> You could either set up a spherical flat-bottom restraint with the
>> origin of that restraint coincident with the COM of the desired
>> residues, or you could use the pull code to set a restraint between the
>> COM of the protein residues and the COM of the ligand.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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