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

[Saravanan]

Thank you.. I hoped it would be simpler. how do I go about creating unified
protein-ligand [moleculartype] directives. Can you suggest any material
available on this topic? that would be extremely helpful.

-Saravanan


On 28 March 2013 16:45, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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