[gmx-users] trjconv and multimers

[David van der Spoel]

On Thu, 2004-11-18 at 09:11 +0100, Anton Feenstra wrote:
> Hi All,
> 
> 
> I've seen similar questions popping up several times on the list, but have not
> seen or found a satisfactory answer(s).
> 
> My problem is with analysis of GroEL: a 21-mer protein complex.
> It runs fine but subunits get separated over the PBC (no problem there).
> 
> This, however, kills the analysis (rmsd's of >10nm...), and should be
> easily fixed with (one of) the pdc option(s) of trjconv.
> 
> Hower, if I do:
> cyp:~/groel > trjconv -s topol.tpr -f traj.xtc -dump 440 -o test.pdb -pbc cluster
> 
> and select 'protein' twice (once for clustering, and once for output), I get:
> 
> Fatal error: Molecule 0 marked for clustering but not atom 4787
> 
Could it be that you have used shuffling?

> 
-- 
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://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++