On 17/09/2012 10:01 PM, tarak karmakar wrote:
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.
It varies, but should be determined by the process by which the rest of
the force field was determined. See
http://www.gromacs.org/Documentation/How-tos/Parameterization
Mark
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