From: siddharth kamal (411cy5084_at_nitrkl.ac.in)
Date: Wed Sep 02 2015 - 08:33:11 CDT
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" <lara.4884_at_gmail.com>
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
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