Hmm... I've been using the 4.0.4 x2top to create OPLS-AA topologies for, e.g., graphane, and it worked more or less right "out of the box", giving very convincing results. What's the problem exactly about recent versions of x2top? I use the -noparams option to leave everything having to do with numbers to grompp. Even periodic boundary conditions for infinite molecules seem to be handled correctly...
2009/7/30 Vitaly V. Chaban <vvcha...@gmail.com> > Giulio, > > I suggest you to try x2top which is spread with gromacs-3.3.1. The > newer versions of x2top are not sain. > > Vitaly > > On Thu, Jul 30, 2009 at 1:48 PM, Giulio Scocchi<giulio.scoc...@icimsi.ch> > wrote: > > Hi Vitaly > > > > Well, I have downloaded it just a couple of months ago, so I guess it > should be 4.0.4 > > > > Giulio > > > > > ---------------------------------------------------------------------------------------- > > > > Giulio Scocchi > > > > iCIMSI - Institute of Computer Integrated Manufacturing for Sustainable > Innovation > > www.icimsi.ch > > DTI - Department of Innovative Technologies > > www.dti.supsi.ch > > SUPSI - University of Applied Science of Southern Switzerland > > www.supsi.ch > > > > Via Cantonale - Galleria 2 > > 6928 Manno > > Switzerland > > tel: +41 (0)58 666 66 46 > > fax: +41 (0)58 666 66 20 > > > > > > -----Messaggio originale----- > > Da: Vitaly V. Chaban [mailto:vvcha...@gmail.com] > > Inviato: giovedì, 30. luglio 2009 12:42 > > A: gmx-users@gromacs.org > > Cc: Giulio Scocchi > > Oggetto: Re: CNT > > > > Hi, > > > > What's the version of your gromacs? > > > > ~ Vitaly > > > >> > >> I am a Gromacs beginner and I am trying to simulate an infinite graphene > >> lattice (see 07.29.09 posts - I don't know how to reply directly to > >> posts, can someone tell me how to do that?). Mark suggested having a > >> look at http://www.gromacs.org/WIKI-import/Carbon_Nanotube . I had > >> already seen that and I hoped there were some kind of more "direct" way. > >> Anyway, I tried to follow the procedure explained in Christopher Stiles > >> website (http://cs86.com/CNSE/SWNT.htm) just to simulate the nanotube > >> (graphene will come). I downloaded all the files and (as it was > >> suggested) typed: > >> > >> > >> > >> x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp > >> > >> > >> > >> and this is what happened: > >> > >> > >> > >> Opening library file > >> /homea/scocchi/GROMACS/share/gromacs/top/aminoacids.dat > >> > >> WARNING: masses will be determined based on residue and atom names, > >> > >> this can deviate from the real mass of the atom type > >> > >> Opening library file > >> /homea/scocchi/GROMACS/share/gromacs/top/atommass.dat > >> > >> Entries in atommass.dat: 178 > >> > >> WARNING: vdwradii will be determined based on residue and atom names, > >> > >> this can deviate from the real mass of the atom type > >> > >> Opening library file > >> /homea/scocchi/GROMACS/share/gromacs/top/vdwradii.dat > >> > >> Entries in vdwradii.dat: 28 > >> > >> Opening library file /homea/scocchi/GROMACS/share/gromacs/top/dgsolv.dat > >> > >> Entries in dgsolv.dat: 7 > >> > >> Opening library file > >> /homea/scocchi/GROMACS/share/gromacs/top/electroneg.dat > >> > >> Entries in electroneg.dat: 71 > >> > >> Opening library file > >> /homea/scocchi/GROMACS/share/gromacs/top/elements.dat > >> > >> Entries in elements.dat: 218 > >> > >> Looking whether force field files exist > >> > >> Opening library file > >> /homea/scocchi/GROMACS/share/gromacs/top/ffoplsaa.rtp > >> > >> Opening library file > >> /homea/scocchi/GROMACS/share/gromacs/top/ffoplsaa.n2t > >> > >> WARNING: all CONECT records are ignored > >> > >> Opening library file > >> /homea/scocchi/GROMACS/share/gromacs/top/ffoplsaa.n2t > >> > >> There are 23 name to type translations > >> > >> Generating bonds from distances... > >> > >> atom 0 > >> > >> > >> > >> ... and at this point it gets stuck. > >> > >> > >> > >> Does anyone have a clue about what I am doing wrong? Could it be that > >> this happens because I am using the most recent version of Gromacs? If > >> so, what should I modify? > >> > >> > >> > >> Thank you! > >> > >> > >> > >> Giulio > > > > > > > > -- > > Vitaly V. Chaban, Ph.D. (ABD) > > School of Chemistry > > V.N. Karazin Kharkiv National University > > Svoboda sq.,4, Kharkiv 61077, Ukraine > > email: cha...@univer.kharkov.ua,vvcha...@gmail.com > > skype: vvchaban, cell.: +38-097-8259698 > > http://www-rmn.univer.kharkov.ua/chaban.html > > =================================== > > !!! Looking for a postdoctoral position !!! > > =================================== > > > > > > -- > Vitaly V. Chaban, Ph.D. (ABD) > School of Chemistry > V.N. Karazin Kharkiv National University > Svoboda sq.,4, Kharkiv 61077, Ukraine > email: cha...@univer.kharkov.ua,vvcha...@gmail.com > skype: vvchaban, cell.: +38-097-8259698 > http://www-rmn.univer.kharkov.ua/chaban.html > =================================== > !!! Looking for a postdoctoral position !!! > =================================== > _______________________________________________ > 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/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/mailing_lists/users.php >
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