[gmx-users] parameter for repeating units with cgenff

gromacs query gromacsquery at gmail.com
Fri Dec 11 16:17:12 CET 2015

Hi All,

I am using cgenff to derive parameters for some polymer (A-BBBB...-C). The
repeating block B has some Oxygen O atom which joins the next residue
(-BO-). When I derive charges for B residue with cgenff then I get net -1
charge on B residue because of this unsatsified O atom. I want to keep B
residue formal charge zero. I get formal charge zero if I derive charges on
B-OH residue but removing H will again will give some non-intergral formal
charge. I am not sure what should done in this regard.

If someone has some experience with this or suggestion I will highly
appreciate it.



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