From: Hemant Kushwaha (
Date: Mon Nov 29 2004 - 01:16:44 CST

I want to simulate protein with ligand inside, the problem is while
running psfgen it always add N and C terminal to the ligand which is
wrong. Has anybody gone through this problem plz let me the solution
of the problem, and also how can i generate psf file using psfgen with
ligand inside the protein.

my psfgen file is as follows:

topology top_all27_prot_lipid.inp
alias residue HIS HSE
alias atom ILE CD1 CD
segment U {
pdb test_protein.pdb
first ACE
last CT3
coordpdb test_protein.pdb U

segment DMV {pdb dmv_clean.pdb}
coordpdb dmv_clean.pdb DMV

segment ION {pdb ion.pdb}
coordpdb ion.pdb ION

alias residue WAT TIP3
segment SOLV {pdb water.pdb}
coordpdb water.pdb SOLV


writepdb test.pdb
writepsf test.psf

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:02 CST