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

[David van der Spoel]

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
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-- 
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
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