AMBER Archive (2003)

Subject: RE: AMBER: carnal iteration deviation from original crd file

From: John (john.dalmaris_at_imperial.ac.uk)
Date: Mon Oct 27 2003 - 19:05:28 CST

Hello Aini, Bill and Vlad,

Thank you very much for your help. I was getting incomplete coord set
for one of my crd files which I should not have used when calculating
the RMSd in the first place. The problem is sorted out now. Thank you
for steering my attention to the right place.

Best wishes,

John

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Bill Ross
Sent: 24 October 2003 16:31
To: amber_at_scripps.edu
Subject: Re: AMBER: carnal iteration deviation from original crd file

> After a simulation I got 11764 frames. But when I used carnal to
calculate
> the RMSd using all my trajectory files (which should add up to 11764)
the
> output file gives me an iteration number of 9798. Does anyone have
any
> idea why this inconsistency?
 
Are you sure the prmtop and crd files agreed on number of atoms?
Were all trajectory files logged as being opened? Was there any
msg at the end about incomplete coordinate set?

Bill Ross

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu