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
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