[gmx-users] retraining multiple protein ligand interactions using pull-code

[Justin Lemkul]

On 3/28/13 4:01 AM, Saravanan wrote:
> Hello everyone,
>
> I am new to using gromacs. I am currently studying an enzyme catalysing a
> transfer reaction. there are two substrates and I want to restraint
> specific interactions between different parts of the ligands and the
> protein. As I understand so far from reading various discussions in the
> group, restraining such interactions is possible through pull code, But we
> can assign only one pull group0, I am wondering if there is better way to
> restraint multiple interactions between multiple molecules in a single
> simulation. If not through pull-code, what will be the best way to ensure
> many specific intermolecular restraints?
>

Use distance restraints.  Unfortunately, this will require a lot of topology 
hacking to create unified protein-ligand [moleculetype] directives.  Restraints 
(like any bonded interaction) can only be applied within a [moleculetype], not 
between them.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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