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.abra...@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 >> -- >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@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 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
