[gmx-users] CHARMM36 parameter for polysaccharide branching
Mohammad Hassan Khatami
mhk302 at mun.ca
Thu May 25 21:00:39 CEST 2017
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:
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?
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