AMBER Archive (2002)

Subject: anal input

From: Prabal Maiti (maiti_at_wag.caltech.edu)
Date: Fri Feb 22 2002 - 18:31:58 CST

Dear Amber Users,
I am trying to use anal to do Energy component analysis (though there is
reported bugs for this feature I wanted to see how it
works. Hopefully AMBER 7 will have everything fixed)) and also
sugar puckering. I have a 10 base pair B-DNA solvated with water and ions.
I used the follwing commands
anal -O -i anal_in_pucker -o anal.out -p double.top -c md_prod.restart

In both cases I get the following output only. It seems anal does not do
anything. At the end of the output I have appended the anal.in file. Can
someone suggest a remedey.

          ---------------------------------------------------------------
          Amber 5.0 ANAL: Static Analysis for Energy/Structure UCSF 1997
          ---------------------------------------------------------------

   1. RESOURCE USE:

     Memory Use Allocated Used
     Real 500000 226150
     Integer 800000 153993 (static)

| Max Nonbonded Pairs: 1292014 packed 2 to a machine word

   2. DATA CONTROL:

  TITLE 'Residue Energy'

     NTX = 1 NTXO = 0 NRC = 0
     NRCX = 0 NGRPX = 20 KFORM = 1

     NTB = 0 BOXX = 51.483 BOXY = 39.715
     BOXZ = 57.527 BETA = 90.000

     NTF = 1 NTID = 0 NTN = 1
     NTNB = 0 NSNB = 50 IDIEL = 1

     RCUT = 12.00 SCNB = 2.00
     SCEE = 1.20 DIELC = 4.00

     IMAX EBMAX EANMAX EDIHMAX ENB14MAX
         1 0.00 0.00 0.00 0.00

     EEL14MAX ENBMAX EELMAX EHBMAX ECONSMAX
         0.00 0.00 0.00 0.00 0.00

   3. A T O M I C C O O R D I N A T E S

          NUMBER OF ATOMS = 11638

--------------------------------------------------------------------------
Below is my anal.in file for two case
TITLE 'Residue Energy'
    1 0 0 0 20 1
    0 51.4828921 39.7147560 57.5269096 90.0
    1 0 1 0 50 1
   12.0 2.0 1.2 4.0
    1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
IOPT 'ENERGY'
RES 1 20
END
STOP

for Sugar Pucker:
TITLE 'Residue Energy'
    1 0 0 0 20 1
    0 51.4828921 39.7147560 57.5269096 90.0
    1 0 1 0 50 1
   12.0 2.0 1.2 4.0
    1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
IOPT 'PUCKER'
0
END
STOP 

-- 
------------------------------------------------------------------------
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)                    
Pasadena, CA 91125                         Fax:626-585-0918
                                           Home add: 110 S. Michigan Ave.
http://www.wag.caltech.edu/home/maiti      Apt # 19, Pasadena, CA 91106
------------------------------------------------------------------------