Including two parameters for protein-ligand simulation

From: Nikhil Maroli (
Date: Wed Oct 28 2015 - 01:52:30 CDT

Dear all,

i wanted to MD after docking i made psf file for ligand using swissparam
server i got ligand.rtf file
using script i made combined psf for the protein+ligand

package require psfgen
topology top_all36_prot.rtf
topology rutin2.rtf
pdbalias residue HIS HSE
segment A {
pdb Ach.pdb
first NTER
last CTER
coordpdb Ach.pdb A
segment B {
pdb rutin.pdb
first NONE
last NONE
coordpdb rutin.pdb B
regenerate angles dihedrals
writepsf new.psf
writepdb new.pdb

now i wanted to do MD for that i have to include the parameter files i have
par_all27_prot_lipid.inp .what i have to do for ligand ?
from server i got ligand.par as parameter file how i include that in namd
configuration file?

im posting this in both namd and vmd-l as it come under both

Nikhil Maroli

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