> I modified the cluster.in as follows.
>
> trajin prod_0-10ns.mdcrd netcdf
> image origin center familiar
> cluster out test-out representative pdb \
> average pdb averagelinkage clusters 5.0 mass rms :1-123 .CA
Get rid of that space in ":1-123 .CA". Also, the PDB's should be fine.
If they are not, there is something funny. Look first at the
representative. It has no averaging.
> I'm inclined to believe that periodic box info has been lost.
Only in the trajectory (as PDB does not have this), but you may not have
dumped a trajectory (with the "all" keyword).
> Are there any fixes for this?
No. I do not think anything is broken, so there is no fix.
Also, imaging alone may not be wise; you need to center your molecule
first...
center :1-123 mass origin
image origin center familiar
Also, calculate the RMSd to convince yourself all is peachy.
rms first mass out rms :1-123
Unless you need the water, I would strip everything but :1-123 as well.
strip :1-123
and use a prmtop that is just the residues 1-123 to look at subsequent
trajectories.
If you are still stuck, I can look into your data more deeply off the
list, noting that I run clustering multiple times a week without problems.
--tec3
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Received on Mon Sep 12 2011 - 14:00:05 PDT
