Re: vmd-l: Including two parameters for protein-ligand simulation

From: Sourav Ray (
Date: Wed Oct 28 2015 - 02:20:04 CDT

It has been going for too long, can you please stop spamming this mailing
list with your inane questions and find someone nearby who knows a bit
about simulations. If not, collect your queries for a day and post them as
a single message. I am surprised no one from UIUC has done anything
regarding the flood of your questions and such an obvious misuse of mailing
list till now. If this keeps on going I will have to subscribe through a
random email id and not my primary one.

In short, if you have no one to guide you and given how good your
comprehension skills are, then maybe simulations is not your cup of tea.

On Wed, Oct 28, 2015 at 12:22 PM, Nikhil Maroli <> wrote:

> 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
> resetpsf
> 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
> guesscoord
> 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
> --
> Ragards,
> Nikhil Maroli

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