[gmx-users] Error in ligand coordinate file
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:
[ system ]
ligand in water
[ molecules ]
where "X" is the number of solvent molecules in the solvated system. Add ions
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users