[gmx-users] How to set restraints for Protein-ligand complex in free energy calculation?

[Justin Lemkul]

On 12/11/19 5:38 AM, Bratin Kumar Das wrote:
> Hi
>     You can use gmx genrestr option for restraining the ligand using same
> force constant. Define the position restrain in topology file. Please
> follow the protein-ligand tutorial of Dr. Lemkul

Absolute position restraints are not what are needed in absolute binding 
free energy calculations. One needs to restrain the relative 
orientation. This used to be accomplished with 
[intermolecular_interactions] and specifications of bonds, angles, and 
dihedrals (or their respective restraints), but it seems that recent 
code changes render that approach nonfunctional. It worked in version 
5.0 or 5.1, but it seems it does not any more.

-Justin

> On Tue 10 Dec, 2019, 11:39 PM Sadaf Rani, <sadafrani6 at gmail.com> wrote:
>
>> I have a protein having two ligands, for which I want to calculate absolute
>> free energy. Could you please suggest me how should I set restraints for
>> two ligands simultaneously?
>> I am trying to do it the first time, any help would really be appreciated.
>>
>> Thanks in advance.
>>
>> Sadaf
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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
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