Thank you for your helpful example. > 在 2016年6月20日,下午11:17,Marlon Sidore <marlon.sid...@gmail.com> 写道: > > 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.
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