patching SO3 group to GAG

From: Lara rajam (
Date: Thu Sep 03 2015 - 19:13:21 CDT

I am trying to generate the psf and pdb file for heparin !
I under stood the issues with the N sulfated glycan.
as initial i tried idoA 2sulfated and 6 sulfated glucosamine.
I took the pdb from 1HPN ( dimer )
my psfgen as below

package require psfgen

topology top_all36_carb.rtf


segment GT1 {

pdb two.pdb


coordpdb two.pdb GT1

patch 14bb GT1:2 CT1:1

patch SUF2B GT1:1

patch SUF6 GT1:2


writepdb dimer.pdb

writepsf dimer.psf


The psf file is not giving the information about the angle and the dihedral
terms for the SO3 group constituting atoms.

Is there any problem in my patching , how to patch it

( is the sulfate molecules are treated as a separate residues in the PDB
file ? )

could any one can explain me .

thanks in advance !

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