Re: AMBER: carnal iteration deviation from original crd file

From: Vlad Cojocaru <>
Date: Fri, 24 Oct 2003 13:32:17 +0200

Are you sure that all your frames are included in the crd traj file?
When you visualize them can you see all of them.....this number is a bit
big so maybe if you do a selection (SELECT MOD 5..lets say) for the
output with Carnal ..might help. Otherwise this shouldnt happen only if
some frames are damaged (at least to my knowledge).

Dalmaris, John wrote:

>Dear Amber Users,
>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?
>Thanks for the help.
>Best wishes,
>The AMBER Mail Reflector
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Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  
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Received on Fri Oct 24 2003 - 12:53:01 PDT
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