[gmx-users] CHARMM36 parameter for polysaccharide branching

[Mohammad Hassan Khatami]

Thanks Justin :) 
It worked.
Small numbers!!!
Best,
MH
> On May 25, 2017, at 3:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 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
> 
> -- 
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
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> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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