RE: parameters problem in sulfated molecules

From: Bennion, Brian (
Date: Tue Sep 01 2015 - 12:27:17 CDT

I would look at your topology and parameter files again. It seems you are missing partial charges (maybe angle parameters are zero) on the sulfate oxygens?
Post your psf and pdb file for the initial structure/topology and pdb of final structure to allow a better chance at other helping you.

From: [] On Behalf Of Lara rajam
Sent: Tuesday, September 01, 2015 10:13 AM
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

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