Re: parameters problem in sulfated molecules

From: siddharth kamal (
Date: Wed Sep 02 2015 - 08:33:11 CDT

Dear Lara
I am also working on heparin structure and facing same problem with heparin structure.
Could you please send me the files you are using for psfgen.


----- Original Message -----

From: "Lara rajam" <>
Sent: Tuesday, September 1, 2015 10:42:42 PM
Subject: namd-l: parameters problem in sulfated molecules

Dear NAMD !
I have already posted this mail , If I can get some help, that will be useful for me !

I am trying to do simulation of heparin disaccharide ( iduronic acid 2 sulfate and nacetyle glucosamine 6 sulfate)
I got the topology file top_all36_carb.rtf and prm files
I built it using vmd and used patch to add glycosidic linkage
I solvated and added counter ions. when I started the minimization and equilibration the SO3 group is disturbed and all the oxygens got merged
I have attached the image for reference(removed solvent molecules). could any one suggest me how to fix this issue

thank you

This mail has been scanned by Cyberoam based UTM at NIT, Rourkela. If your mail still contains virus forward it to ""

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:22:02 CST