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

[Mark Abraham]

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