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

[Justin Lemkul]

On Thu, Mar 28, 2013 at 8:18 AM, Saravanan <msrvnn+gmx at gmail.com> wrote:

> 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.
>
>
Depending on the complexity of the ligand, you may be able to do it by hand
by simply adding the ligand parameters after the protein in all relevant
directives of the Protein [moleculetype]. Otherwise, you will need to
create an .rtp entry for the ligand and use pdb2gmx command line options to
create the merged topologies (using, e.g. chain identifiers to indicate
that they should be placed in the same [moleculetype] directive). In this
case, refer to
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
.

This is a rather advanced topic, so do as much tutorial material and other
simulations as you can to familiarize yourself with a "standard" Gromacs
workflow. You should also read Chapter 5 of the manual thoroughly to
understand topology organization.

-Justin

-- 

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

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