AMBER Archive (2002)

Subject: helix analysis

From: Prabal Maiti (maiti_at_wag.caltech.edu)
Date: Mon May 20 2002 - 14:20:45 CDT

I am trying to analyse helical paprameters for a 10-mer B-DNA (1bd1 pdb
code). I have the topology file created by xleap and several restart file
created through ptraj form AMBER trajectory file.
Below is my anal.in file

TITLE 'Helix parameter'
    1 0 0 0 22 1
    0 51.4828921 39.7147560 57.5269096 90.0
    1 0 1 0 50 1
   0.0 2.0 1.2 1.0
    0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
HELIX
0 0 0 0 0
STOP

However it exits saying
THE DNA IS NOT A STANDARD TYPE ... NSTRAND = 0

I used AMBER95 FF.
Can someone susggest whats happening and possibly send me a coorect
anal.in file.

Thanks
Prabal 

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Prabal K Maiti                             Email:maiti_at_wag.caltech.edu
Beckman Institute (139-74)                       pkmaiti_at_yahoo.com
California Institute of Technology         Tel:626-395-8151 (O)
400 South Wilson Avenue                       :626-744-1363 (H)                    
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