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 <[email protected]> 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
