[gmx-users] gmxdemo: peptide to real protein and boom
hotafin at gmail.com
Tue Feb 14 20:16:54 CET 2006
Check out what groups you have. The values at tau_t and ref_t refer to those
In the default case, in the demo, those refer to "protein" and "SOL" groups.
On 2/14/06, David Mathog <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???
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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