> 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.
The cluster routine does not "alter" the coordinates per se so there must
be some mismatch,
try
trajin prod_0-10ns.mdcrd 1 2 1
trajout test pdb
and look at these. If PDB number 2 is messed up, then it is a prmtop
mismatch. Alternatively, perhaps molecules have "shifted" due to periodic
imaging and you need to image prior? [Note also that the average
structure may of course have funny bonds since motional averaging will
lead to not representative structures.]
For the "structures" from the clustering, if you looking at a trajectory
(not the pdb's), box information could be absent.
Note also in that clustering command the space in the cluster mask may
not be tolerated.
cluster out test-out representative pdb \
average pdb averagelinkage clusters 5.0 mass rms :1-123.CA
^
--tec3
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Received on Mon Sep 12 2011 - 12:30:02 PDT
