VMD-L Mailing List

From: MUNUBARTHI KRANTHI KUMAR (k.munubarthi_at_iitg.ac.in)
Date: Sun Jan 12 2020 - 23:11:30 CST

I am trying to generate alternate block polymer of Alginate with G and M block monomers.
I have followed the following steps:

1.Generated initial GM block structure using Avogadro having neutral charge
2.Uploaded the structure in pdb format in LigParGen to generate topology and parameter files (OPLS) for NAMD.
3. I have removed the required H and O atoms in the GM block and then bonded the resultant structure with other GM using topotools.
4.Required sequence is: GMGMGMGMGM

Problem: after generating the entire structure, charge is not neutral

Please help me in solving the charge assignment issue during the monomer linkage

Thank You.

Regards
M. Kranthi Kumar