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

From: Prabal Maiti <>
Date: Thu 31 Jan 2002 11:49:00 -0800 (PST)

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.

Prabal K Maiti                   
Beckman Institute (139-74)             
California Institute of Technology         Tel:626-395-8151 (O)
400 South Wilson Avenue                       :626-744-1363 (H)                    
Pasadena, CA 91125                         Fax:626-585-0918
                                           Home add: 110 S. Michigan Ave.      Apt # 19, Pasadena, CA 91106
Received on Thu Jan 31 2002 - 11:49:00 PST
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