[gmx-users] trjconv and multimers

[Anton Feenstra]

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


-- 
Groetjes,

Anton
   _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Room P275  Tel: +31 20 44 47608  Fax: +31 20 44 47610 |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "It Wouldn't Hurt to Wipe Once In a While" (Beavis and|
|             | Butthead)                                             |
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