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
