From: Ross Walker <>
Date: Sun, 18 Mar 2007 22:09:56 -0700

Set 1000
ERROR in readAmberTrajectory(): Set #1001 is corrupted (

This is an innocuous error - you can ignore it. Essentially the mdcrd file does not specify how many frames it contains and if you didn't tell ptraj how many frames to read, on the trajin line, it will just keep reading before it reads past the end of the file. However, if you expect your trajectory file to contain more than 1000 frames then it could well be corrupted...
Either way you should have got the rmsd data for 1000 frames.
PTRAJ RMS: dumping RMSd vs time data
[root.amber BSM]#

On another note, it really isn't advisable to run things as root on a Linux box...
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| <> | PGP Key available on request |

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Received on Wed Mar 21 2007 - 06:07:14 PDT
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