RE: Regarding problem in psfgen of heparin

From: Tristan Croll (
Date: Mon Oct 05 2015 - 23:00:32 CDT

Hi Siddharth,

Check the coordinates of the oxygen atom that's out of position. Is it at (0,0,0) by any chance? That will happen if your residue is missing an atom (or an atom is misnamed) and the patch doesn't include internal coordinates to build correctly. The important question is: what happens when you try to run an energy minimization in NAMD? Does it pop back into place, or does the simulation crash?



-----Original Message-----
From: [] On Behalf Of siddharth kamal
Sent: Saturday, 3 October 2015 5:20 AM
To: namd-l; owner-namd-l
Subject: namd-l: Regarding problem in psfgen of heparin

Dear user's
 I am trying to generate the psf and pdb file of heparin. In structure the sulfated amine part is showing problem problem.

Here the psfgen script i am using

package require psfgen
topology top_all36_carb_c.rtf
segment CT {
pdb HPN_1.pdb
coordpdb HPN_1.pdb CT
patch SUF6 CT:1
patch NHSHB CT:1

writepdb final_HP.pdb
writepsf final_HP.psf

please see images in the attachment and try to help me out.

Thanking you

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