[gmx-users] CHARMM36 parameter for polysaccharide branching

Justin Lemkul jalemkul at vt.edu
Thu May 25 21:29:52 CEST 2017

On 5/25/17 3:00 PM, Mohammad Hassan Khatami wrote:
> Hello!
> I am trying to simulate a simple branching polysaccharide molecule. Thanks to you, I found and implemented the CHARMM36 parameters for the 1->4 and 1->6 links, however, I was not able to find the exact partial charge parameters for the monomer in the branching point of the polymer. In other words, I am looking for parameters for the monomer AAA(the name is arbitrary), below:
>                          1->6 —AGM—1->4—AGF
>                         /
> AGI—1->4—AAA—1->4—AGF
> I have combined the parameters for 1->4 (14ba) and 1->6(16ab) links from top_all36_carb.rtf  and the simulation is running with all bonds and links in place, but the total charge of the system is not zero (which it should). My only concern is if specific parameters for the monomer in the branching point of the polymer, exists, and where can I find them?

The same place as you got the linkages; all the PRES entries I pointed out 
before (as well as the 1-6 linkages) have the correct charges and types 
specified.  Your charge should come out to net neutral, as the branching doesn't 
impose any net charge.  Check your work carefully.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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