[gmx-users] gmxdemo: peptide to real protein and boom

[Tamas Horvath]

if you have ions in your system, and you are using 2 groups, try define them
as protein & non-protein.

Don't modify the source without knowing what u are doing. Gromacs can handle
your groups... Take some time to read the manuals...

On 2/14/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Tamas Horvath wrote:
> > Check out what groups you have. The values at tau_t and ref_t refer to
> > those groups.
> > In the default case, in the demo, those refer to "protein" and "SOL"
> > groups.
>
> Indeed, there are probably ions in the pdb file.
>
> >
> > On 2/14/06, *David Mathog* <mathog at caltech.edu
> > <mailto:mathog at caltech.edu>> wrote:
> >
> >     I'm still struggling with gromacs.  The gmxdemo script runs.
> >     So I tried to scale up a bit and chose more or less at random a
> >     protein with some CYS-CYS bonds (H2MCM.PDB) and tried to plug it
> >     into the gmxdemo script instead of "cpeptide".
> >
> >     No Joy.
> >
> >     It eventually comes completely off the rails at the grompp pr
> section
> >     where it comes up with this gem:
> >
> >     Fatal error:
> >     Not enough ref_t and tau_t values!
> >
> >     pr.mdp has these lines:
> >
> >     tau_t         =   0.1    0.1
> >     ref_t         =   300    300
> >
> >     which are straight from the gmxdemo script.
> >
> >     The 3.2 manual has no matches on "tau_t" or "ref_t".
> >
> >     It looks like the programs wants more columns on these lines, but
> >     how many, and why that many???
> >
> >     Thanks,
> >
> >
> >     David Mathog
> >     mathog at caltech.edu <mailto:mathog at caltech.edu>
> >     Manager, Sequence Analysis Facility, Biology Division, Caltech
> >     _______________________________________________
> >     gmx-users mailing list    gmx-users at gromacs.org
> >     <mailto:gmx-users at gromacs.org>
> >     http://www.gromacs.org/mailman/listinfo/gmx-users
> >     Please don't post (un)subscribe requests to the list. Use the
> >     www interface or send it to gmx-users-request at gromacs.org
> >     <mailto:gmx-users-request at gromacs.org>.
> >     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >     <http://www.gromacs.org/mailing_lists/users.php>
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060214/3dbe8fb0/attachment.html>