- > Message: 1 > Date: Thu, 9 Dec 2010 23:16:21 -0500 > From: Vitaly Chaban <vvcha...@gmail.com> > Subject: [gmx-users] Re: Which FF could be used for protein-RNA MD > simulation in GROMACS? > To: gmx-users@gromacs.org > Message-ID: > <aanlktik995o98r7gm8-klac0xuf9m3rb_43+31afa...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hey, Shiyong - > > I believe your problem is related to X2TOP usage rather than to a > proper force field choice. I'd suggest to start with looking into N2T > files for the below entries. > > Cheers. > > -- > Dr. Vitaly V. Chaban > Rochester, U.S.A. > > > > I just tried G53a6 for protein-RNA simulation. But fatal error shows > up. > > > > Opening library file /usr/share/gromacs/top//FF.dat > > > > Select the Force Field: > > 0: GROMOS96 43a1 force field > > 1: GROMOS96 43a2 force field (improved alkane dihedrals) > > 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) > > 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) > > 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) > > 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) > > 6: [DEPRECATED] Gromacs force field (see manual) > > 7: [DEPRECATED] Gromacs force field with hydrogens for NMR > > 8: Encad all-atom force field, using scaled-down vacuum charges > > 9: Encad all-atom force field, using full solvent charges > > > > Best > > > > -- > > Shiyong Liu > > > ------------------------------
Dear Shiyong Liu, I have run across RNA/DNA .itp/.rtp files by searching (for a while) on the internet, a year or so back, which are/were compatable with the G53a6 FF. Aside from that though, I don't remember which lab/site had them. The same is true for lipid and carbohydrate .itp/.rtp libraries. Stephan Watkins -- GMX.ch - Schweizer FreeMail-Dienst mit über 800.000 Mitgliedern E-Mail & mehr! Kostenlos: http://portal.gmx.net/de/go/chfreemail -- 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
