AMBER Archive (2004)

Subject: AMBER: Problem with AMBER/ANAL

From: Daniel Wetzler (danielwetzler_at_appleinfo.de)
Date: Fri Oct 08 2004 - 03:31:29 CDT

Hallo,

I 'm trying to calculate the binding enrgy of a ligand to
a protein using ANAL.
Therefor I created the following configuration file, which I basically
copied from a former Mailing :

TITLE 'Test'
    1 0 0 0 20 1
    0 51.4828921 39.7147560 57.5269096 90.0
    7 0 1 0 50 1
   12.0 .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'
protein
RES 1 277
END
ligand
RES 278-279
END
END
STOP

If I start AMBER I only get the following output :

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

   1. RESOURCE USE:

| INFO: Old style PARM file read

     Memory Use Allocated Used
     Real 500000 73027
     Integer 800000 149048 (static)

     Max Nonbonded Pairs: 650952 packed 1 to a machine word

   2. DATA CONTROL:

  TITLE 'Test'

     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 = 7 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

mod2

          NUMBER OF ATOMS = 3992

But I don't get any calculations.
Does anyone know what could be wrong ?
Since I don't get any Error I don't know what to change.
Could it be a problem with the box ?

Hope someone can help..

Best wishes,

Daniel Wetzler

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