AMBER Archive (2003)

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

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Fri Oct 24 2003 - 07:42:24 CDT

Well, usually damaged frames come from unproper finish of the jobs
(especially if you did several restarts or so if something crashed and
the coordinated were droped only partially for instance)...I had once
such a problem....did you look at the carnal output ...usually it tell
you what happens. But on the other hand is hard for me to get why do you
need all the frames (especially with such a number of them) so..if you
just do a select as I told you (see amber manual) and output only 5th or
2nd frame and see if you get the corrrect number. Now of course there
might an intrinsec problem of Carnal with handling so many frames but
that I am not aware of because I had never dealt with so many frames.
Sorry for not being able to tell you more..maybe some other people will...
Good luck
Vlad

Dalmaris, John wrote:

>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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