Hi, What you want is to convert these from amber (kcal) to gromacs (kJ). I followed successfully another post from the mailing list here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-September/101115.html
What you should do is make sure your conversion is right, by taking an example from the amber forcefield in amber format and its equivalent in gromacs format, before applying that conversion on your new parameters. Hope that helps. Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-06-20 16:22 GMT+02:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > It sounds like what you want to look for is the documentation for those > file formats. > > Mark > > On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote: > > > Hi, > > I am simulating a protein phosphorylated on Ser and Thr residues using > > AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the > > phophorylation parameters in the > > http://sites.pharmacy.manchester.ac.uk/bryce/amber < > > http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is > > difficult for me to read the parameters and statistics in the frcmod and > > off files. So I have trouble in converting the statistics in framod files > > and off file to gromacs files, such as .rtp, ffbond.itp. > > > > Best regards, > > Ouyang > > -- > > 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.
