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GLYCAM-L  July 2017

GLYCAM-L July 2017

Subject:

Fw: Heparin Amber parameters from online GLYCAM builder

From:

"B. Lachele Foley" <[log in to unmask]>

Reply-To:

Users of GLYCAM & GLYCAM-Web <[log in to unmask]>

Date:

Thu, 13 Jul 2017 20:20:15 +0000

Content-Type:

text/plain

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text/plain (51 lines)

I guess you looked in http://glycam.org/docs/forcefield/all-parameters/ ?  You probably need the regular GLYCAM files (but not GLYCAM EP) as well as the files under "Special Releases".  

For most of the residues you mention, we consider the sulfates to be separate residues.  If you were considering them as a single entity, the link below explains how to add derivatives:

http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
 
If that isn't the information you need, tell me which particular residues you aren't finding and I'll try again.

 :-) Lachele

Dr. B. Lachele Foley
Associate Research Scientist
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
[log in to unmask]
http://glycam.org
  



From: Bill Miller III <[log in to unmask]>
Sent: Wednesday, June 28, 2017 8:55 PM
To: [log in to unmask]
Subject: Heparin Amber parameters from online GLYCAM builder
† 

Hi,
Iím trying to start a new research project simulating heparin with some bound ligands. I used your online GLYCAM builder (http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=8)  to build an overall heparin structure, but I am having some difficulties re-creating the heparin prmtop/restart files using tleap. I tried to use ParmEd to make the necessary library/frcmod files from the GLYCAM builder prmtop so that I could convert the heparin  PDB to Amber prmtop/restart files. I sourced the ParmEd library/frcmod file in tleap to create new heparin prmtop/inpcrd files, but I was unsuccessful (specifically, tleap isnít connecting all the residues together; almost like the head/tail atoms arenít defined  properly). So I think I am missing some important force field parameters.
Anyway, I was hoping you would be willing to share the Amber library/prep/frcmod files that are necessary to build the Amber force field parameters for heparin? Primarily, the parameters for the heparin monosaccharides  residues listed on the online GLYCAM builder (http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=8):
monosaccaride 1: GlcNAc, GlcNAc(3S), GlcNAc(6S), GlcNAc(3S,6S), GlcNS, GlcNS(6S), GlcNS(3S), GlcNS(3S,6S)

monosaccaride 2: GlcA, GlcA(2S), IdoA, IdoA(2S), dUA, dUA(2S)
Aglycon: -OH, -OME, -OtBu
I tried looking on the GLYCAM website for the proper files to download for these residues, but I could only find downloadable force field files for a few of the total residues.
This would really help us out as we are trying to start a collaboration with an experimental group.†
By the way, the online GLYCAM builder is fantastic! If it werenít for that resource, I would be nowhere near as far along as I am now.

Thanks for your time.
-Bill


 -- 




Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952           

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