[gmx-users] charge calculation........
erikm at xray.bmc.uu.se
Tue Sep 18 20:09:35 CEST 2012
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.).
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 ?
> 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
>> gmx-users mailing list gmx-users at gromacs.org
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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
More information about the gromacs.org_gmx-users