On 8/9/12 6:31 AM, sai nitin wrote:
Hi justin,
Yes swiss param gave me ligand.itp file which gromacs topologies i
included in topol.top file which i generated ..usign PDB2GMX so no
need of creating seperate topol.top file for ligand only? can i use
same topol.top file to run MD to simulate only ligand because current
topol.top file has topologies for both ligand and protein..
If you have an .itp file for the ligand, you create a new topol.top by hand.
It's very simple:
#include "charmm27.ff/forcefield.itp"
#include "ligand.itp"
#include "charmm27.ff/tip3p.itp"
[ system ]
ligand in water
[ molecules ]
LIG 1
SOL X
where "X" is the number of solvent molecules in the solvated system. Add ions
as necessary.
-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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