Hi, As I think Justin said a few days ago, force fields are typically parameterized for proteins, so THR means the dipeptide moiety, not e.g. the zwitterionic one. The latter would need many of the atoms to have different charges. It's essentially a different molecule, and one which the force field designers might or might not have felt important to target. If you need the standalone amino acids, then you should choose your force field (plus perhaps topology+parameter generation strategy) with that in mind, rather than assuming that any particular force field is appropriate, and then trying to make your square problem fit in that round hole.
Mark On Mon, Oct 30, 2017 at 5:04 PM rose rahmani <rose.rhm...@gmail.com> wrote: > yes of course > > On Mon, Oct 30, 2017 at 7:27 PM, R C Dash <rcdash0...@gmail.com> wrote: > > > can you please upload your PDB file? > > > > On Mon, Oct 30, 2017 at 11:41 AM, rose rahmani <rose.rhm...@gmail.com> > > wrote: > > > > > 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. > > > > > -- > > 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.
