AMBER Archive (2002)

Subject: LIMIN Faliure/Energies per residue for B-DNA etc.

From: Prabal Maiti (maiti_at_wag.caltech.edu)
Date: Thu Jan 31 2002 - 13:49:00 CST

Dear Amber users:
I dowloaded a PDB file for a crystal str. of B-DNA from Protein data bank
and thorugh Leap I added Na+ ions and then solvated it. After that I ran
minimization with PME. After 250 minimization steps it crashed saying
"REPEATED LINMIN FAILURE". I changed the BOX dimension (make it larger) by
hand in the prmtop file (a suggestion in the AMBER home page). But same
things happened but after 290 steps. Any solution.

Anyway I took the minimized str. after 290 minimization steps and started
running MD with sander for 500ps.

Now I want to calculate energy for each residue for the DNA and also
want to compute the helical parameters. Is it
possible? Looking at manual it seems I can do it by ANAL. However my
initial try failed. So can someone send me a proper 'analin' file and also
explain (please be explicit) how to do this.
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)
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