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

[Erik Marklund]

As mentioned, you should make RESP charges for AMBER parameters. ESP parameters are furthermore often a bit bizarre (aliphatic carbons with charge well below -1etc.).

Erik

14.11 skrev tarak karmakar:

> 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 ?
> 
> Thanks,
> Tarak
> 
> 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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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html