[gmx-users] Re: CNT

[Vasilii Artyukhov]

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 <vvchaban at 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.scocchi at 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:vvchaban at gmail.com]
> > Inviato: giovedì, 30. luglio 2009 12:42
> > A: gmx-users at 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: chaban at univer.kharkov.ua,vvchaban at 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: chaban at univer.kharkov.ua,vvchaban at gmail.com
> skype: vvchaban, cell.: +38-097-8259698
> http://www-rmn.univer.kharkov.ua/chaban.html
> ===================================
> !!! Looking for a postdoctoral position !!!
> ===================================
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