AMBER Archive (2003)

Subject: Re: AMBER: large file for carnal

From: volodya (volodya_at_imb-jena.de)
Date: Sun Oct 05 2003 - 06:23:44 CDT

I have:

Linux klingsor.imb-jena.de 2.4.18-3smp #1 SMP Wed Nov 27 12:26:38 CET 2002 i686 unknown

Red Hat Linux release 7.3 (Valhalla)

amber7, compiled using gcc 3.2.1 and machine-file Machine.g77_mpich

I started with:

FILES_IN
  PARM p1 1tubg_min3.top;
  STREAM s1 mdpme4_g.mdcrd;
FILES_OUT
  TABLE tab1 rms_to_start;
DECLARE
  GROUP gALL (RES 1 - 440);
  RMS r1 FIT gALL s1;
OUTPUT
  TABLE tab1 r1;
END

Output:

- CARNAL -
                          AMBER 6.0

                      COORDINATE ANALYSIS

input stdin

>> FILES_IN
>> PARM p1 1tubg_min3.top;
>
Reading parm file (1tubg_min3.top)
parm: opening 1tubg_min3.to

>> STREAM s1 mdpme4_g.mdcrd;
>
Using default parm (1tubg_min3.top) for STREAM s1
(box will be read from stream)
stream: opening mdpme4_g.mdcrd
mdpme4_g.mdcrd: sys err Value too large for defined data type

Can other programs open the file?

I can open the file with VMD and load some frames.

Bill Ross wrote:

>>I have very large mdcrd file with trajectories - 11 GB. Carnal can not
>>open this file for analysis. What should I do?
>>
>
>What is your carnal cmd file, and what output? What computer?
>Can other programs open the file?
>
>Bill Ross
>
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-- 
Volodymyr Nechiporuk-Zloy
Institute of Molecular Biotechnology <http://www.imb-jena.de>
Dept. Single Cell and Single Molecule Techniques 
<http://www.imb-jena.de/www_kog/>
Beutenbergstrasse 11
D - 07745 Jena
Germany
Phone: *49 3641 656169
Fax:      *49 3641 656166

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