AMBER Archive (2003)

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

From: Dalmaris, John (john.dalmaris_at_imperial.ac.uk)
Date: Fri Oct 24 2003 - 07:29:28 CDT

Thanks for the input Vlad. Yes, all the frames are there (based on VMD).
Damaged frames is the most possible explanation. What causes the frames to
be damaged? Since carnal can recognise them can we do the same and exclude
them from any calculation?

Many thanks,

John

-----Original Message-----
From: Vlad Cojocaru
To: amber_at_scripps.edu
Sent: 10/24/2003 12:32 PM
Subject: Re: AMBER: carnal iteration deviation from original crd file

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).
Vlad

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,
>
>John
>
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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 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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