From: Aditi Gotkhindikar (aditi.got_at_gmail.com)
Date: Mon Dec 27 2021 - 22:33:03 CST

---------- Forwarded message ---------
From: Aditi Gotkhindikar <aditi.got_at_gmail.com>
Date: Mon, Dec 27, 2021 at 5:49 PM
Subject: vmd-l: issue with protein- ligand psfgen
To: <vmd-l_at_ks.uiuc.edu>

Hello sir,
I have a protein-ligand docked complex. I have generated the topology for
both protein and ligand separately. Using the psfgen script and both
topology files, I tried making the complex pdb and psf but there is a loss
of oxygen and 2 carbon atoms from the ligand. Hence tried generating psf
and pdb only for ligand which also gave the same above problem (PFA the
script file for this - lig_psfgen.pgn)

The script used is as below (complex_psfgen) -
######################
package require psfgen
topology top_all36_prot.rtf
topology rbge.rtf
segment PROT {
first NONE
last NONE
pdb pro.pdb
}
coordpdb pro.pdb PROT
segment LIG {
first NONE
last NONE
pdb rbge_final.pdb
}
coordpdb rbge_final.pdb LIG
guesscoord
writepsf rbge_comp.psf
writepdb rbge_comp.pdb
############################

PFA the ligand pdb and topology below.

Thank you
Aditi.