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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Sep 17 14:51:43 CEST 2012

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 


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