Re: parameters problem in sulfated molecules

From: Peter Freddolino (
Date: Tue Sep 01 2015 - 12:25:02 CDT

Dear Lara,
My guess is that at some point the angles and dihedrals weren’t generated properly, thus allowing the sulfur oxygens to go right on top of each other. It would help if you post the psfgen script that you used.

> On Sep 1, 2015, at 1:12 PM, Lara rajam <> wrote:
> 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
> <Screen Shot 2015-08-29 at 9.51.39 AM.png>

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