From: Axel Kohlmeyer (
Date: Sat Nov 06 2010 - 16:54:53 CDT

On Sat, 2010-11-06 at 16:43 -0400, vani panguluri wrote:
> Hello,
> Can anyone help how to merge the ligand and protein??
> I had done that merging manually but i was unable to see the ligand
> when i had converted that pdb file into psf file by using automatic
> psf builder.

you already had several suggestions. how many more do you need?

how about this?
which uses psfgen as a backend.

also topotools was already suggested which can
do pretty much the same thing via loading the
individual files into separate molecules and
then do some script magic in ::TopoTools::mergemols

if you want good help you have give people
feedback on their suggestions.

> can any one help me with some suggestions because i need to complete
> this one as early as possible.

well, first of all that is _your_ problem;
_everybody_ needs to get stuff done.

the rule of the thumb is that you get better help
not by telling people how desperate you need it,
but rather by making it easy to help you or at
least demonstrate that you are willing to invest
more than a minimal effort.


> please provide me some suggestions.
> Thanks & regards,
> Vani

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.