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

tarak karmakar tarak20489 at gmail.com
Tue Sep 18 14:11:31 CEST 2012

Thanks Mark.

I have gone through the link "Parameterization of novel molecules" and
I see quantum calculations can be handy for this type of charge
calculation (AMBER). So for the unprotonated tyrosine, I am taking two
more amino acids (left and right) and calculating ESP charges of the
tri-peptide by using HF / 6-31(+)g(d) level of theory. Can you please
tell me whether I can include the partial charges of all the atoms of
the middle tyrosine (unprotonated) in the aminoacids.rtp file to
simulate the protein ?


On Mon, Sep 17, 2012 at 6:21 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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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