if it is included,so why AMBER doesnt identify amino acids like THR? error is such 'X' residuetype is not found in residue topology database?!!!! i dont know what is the problem?
thanks for your attention On Mon, Oct 30, 2017 at 6:25 PM, R C Dash <rcdash0...@gmail.com> wrote: > use https://atb.uq.edu.au/index.py / > http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg / or > http://swissparam.ch/ > or http://vienna-ptm.univie.ac.at/ for .itp file > All amino acids are identified bybby AMBER force field. If you there is > some modification like methylated lysine you have to creat a lib file and > use it in tleap AMBERTools. > > On Mon, Oct 30, 2017 at 10:48 AM, Tasneem Kausar < > tasneemkausa...@gmail.com> > wrote: > > > You only need a pdb file for amino acids/proteins. pdb2gmx in gromacs > does > > the job of making itp. > > > > <https://www.avast.com/sig-email?utm_medium=email&utm_ > > source=link&utm_campaign=sig-email&utm_content=webmail> > > Virus-free. > > www.avast.com > > <https://www.avast.com/sig-email?utm_medium=email&utm_ > > source=link&utm_campaign=sig-email&utm_content=webmail> > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > > On Mon, Oct 30, 2017 at 8:11 PM, rose rahmani <rose.rhm...@gmail.com> > > wrote: > > > > > hello > > > > > > how can i make an .itp file for amino acids? > > > which amino acids is identified in AMBER forcefield? > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at http://www.gromacs.org/ > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
