Re: [AMBER] ptraj clustering

From: Thomas Cheatham III <tec3.utah.edu>
Date: Mon, 12 Sep 2011 14:37:55 -0600 (Mountain Daylight Time)

> 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

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 12 2011 - 14:00:05 PDT
Custom Search