[gmx-users] Error in ligand coordinate file

Justin Lemkul jalemkul at vt.edu
Thu Aug 9 13:09:46 CEST 2012

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 ]

where "X" is the number of solvent molecules in the solvated system.  Add ions 
as necessary.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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