Re: Including two parameters for protein-ligand simulation

From: Abhishek TYAGI (
Date: Wed Oct 28 2015 - 01:59:21 CDT

Dear Nikhil,

Have you done tutorials available in NAMD. It will give you all idea about how to use all these files, and using swissparam server is not good idea you may use VMD to build your files. Have a look on mailing list experts have suggested many good ways.


From: <> on behalf of Nikhil Maroli <>
Sent: Wednesday, October 28, 2015 2:52 PM
To:; Vmd L
Subject: namd-l: Including two parameters for protein-ligand simulation

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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