Hi everybody,
I've been trying to cluster a 10ns trajectory using
ptraj solvated.prmtop cluster.in
where cluster.in is:
trajin prod_0-10ns.mdcrd
cluster out test-out representative pdb \
average pdb averagelinkage clusters 5.0 mass rms :1-123 .CA
Clusters are produced as expected, however, when I try to visualise the clusters (e.g. test-out.c1) using the original solvated.prmtop file produced by tleap, bond lengths, etc. are mangled.
I'd appreciate any ideas why should this be so.
All the best
George
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Received on Mon Sep 12 2011 - 08:30:02 PDT
