[gmx-users] constraining charges

gromacs query gromacsquery at gmail.com
Sat Oct 17 16:56:05 CEST 2015

Hi All,

I have some amino-acid residue in which some extra side chain(s) attached
by replacing H from amino-acid. I want to simulate this with CHARMM ff.
Somehow I can choose best bonded params.

But in order to keep integral charge on this modified aminoacid I was
thinking if there is any way to derive charges of the side chain whose
formal charge (net partial charge) be equal and opposite to net charge on
amino-acid with removed Hydrogen. I saw Cgenff is available but it can not
constrain some net charge and some times it does not work because of some
non-acceptable functional groups or bonds.

Please suggest, Thanks


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