[gmx-users] trjconv and multimers
David van der Spoel
spoel at xray.bmc.uu.se
Thu Nov 18 09:28:49 CET 2004
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 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
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