[gmx-users] changing charged groups in CHARMM RNA

maria goranovic mariagoranovic at gmail.com
Tue Mar 22 14:42:39 CET 2011

Dear List

I was looking at the charged groups in a charmm nucleotide, and could see
several groups containing 4 to 14 atoms with integer charges. However, the
default topology does not have these charged groups. each atom is given a
charged group in the default topology. Can we foresee any problems in
replacing the default charged groups generated by pdb2gmx by custom-made
charged groups of integer values ? Along the same lines, will this lead to a
significant increase in performance, besides the advantage of
transferability ?

Thanking you in advance


Maria G.
Technical University of Denmark
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