[gmx-users] charge calculation........

tarak karmakar tarak20489 at gmail.com
Mon Sep 17 14:01:10 CEST 2012

Dear All,

             I want to have one of tyrosine residues in my protein to
be unprotonated. I am using amber force field for the simulation. But
in aminoacid.rtp there is no entry for the unprotonated one. So I am
adding it by myself in to the .rtp file. Now I am bit confused with
the charge of the unprotonated one. How can I calculate the partial
charges for each and every atoms in  unprotonated tyrosine? Would
Gaussian/SCF be a good one to deal with this matter? Should I take the
tyrosine amino acid alone to calculate the charge in Gaussian ?
Please suggest me the proper method(s) to calculate the charge.



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