Hi everybody,
I'm trying to cluster the trajectory frames of a 2ns production run of a solvated complex (138 residues).
Using ptrja my.prmtop cluster.in
where cluster.in is
trajin prod_2ns.mdcrd
center :1-138 mass origin
image origin center familiar
cluster out test-out representative pdb \
average pdb averagelinkage clusters 5.0 mass rms :1-138 .CA
produces clusters. However, when I try to visualise the clusters some frames show with unrealistic bond lengths.
I believe the problems is in the centering and imaging.
I'd appreciate if anyone could help to correct the above script.
Thanks in advance
George
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Aug 20 2011 - 04:30:02 PDT
