AMBER Archive (2002)

Subject: Re: Energy decomposition with ANAL

From: Numan Oezguen (numan_at_bohr.utmb.edu)
Date: Fri Dec 06 2002 - 11:08:20 CST

Dear all,

First I would to thank David Case for the response/hint about the GROUP keyword.
Unfortunately removing this keyword from the anal.in file didn't change the
output at all. Is there anyone who have used ANAL to do energy decomposition, or
is it only a non working relict taken over from earlier AMBER version? By the
way I am still using AMBER6. How can I get the different energy contribution for
a given snapshot of the MD-runs?

Here again my original question:
I am doing MD-Simulation on a system with a protein, DNA, Mg2+ and water.
Dependent on the initial position of Mg2+ it's moving during the simulation. I
want to know what are the driving forces, what are the energy contributions of
the surrounding residues. To my understanding the ANAL program should be used
for such analysis. As parameter file I use the *.top file generated with XLEAP
and the coordinate input file is the last restart file of the MD run.

Appreciate any help/comment

Numan

 I execute this command:
=================================================================
anal -O -i anal.in -o anal.out -p md16.top -c md16.rst
=================================================================

Here is my anal.in:
=================================================================
Magnesium interactions
    1 0 0 0 70 1
    2 62.6413970 79.2115252 58.4662127 0
    1 0 2 1 9999 1
 999.0 2.0 1.2 1.0
 1 -1.0E40 -1.0E40 -1.0E40 -1.0E40 -1.0E40 -1.0E40 -1.0E40 -1.0E40 -1.0E40
 ENERGY
 GROUP
 Mg
 RES 299
 END
 Protein
 RES 1 298
 END
 END
 STOP
=================================================================

And here is the output anal.out:
=================================================================
---------------------------------------------------------------
          Amber 5.0 ANAL: Static Analysis for Energy/Structure UCSF 1997
          ---------------------------------------------------------------

   1. RESOURCE USE:

     Memory Use Allocated Used
     Real 5000000 597834
     Integer 5000000 500933 (static)

| Max Nonbonded Pairs: 8998134 packed 2 to a machine word

   2. DATA CONTROL:

   Magnesium
interactions

     NTX = 1 NTXO = 0 NRC = 0
     NRCX = 0 NGRPX = 70 KFORM = 1

     NTB = 2 BOXX = 62.641 BOXY = 79.212
     BOXZ = 58.466 BETA = 0.000

     NTF = 1 NTID = 0 NTN = 2
     NTNB = 1 NSNB = 9999 IDIEL = 1

     RCUT = 999.00 SCNB = 2.00
     SCEE = 1.20 DIELC = 1.00

     IMAX EBMAX EANMAX EDIHMAX ENB14MAX
         1 -inf -inf -inf -inf

     EEL14MAX ENBMAX EELMAX EHBMAX ECONSMAX
         -inf -inf -inf -inf -inf

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

                                                                                

          NUMBER OF ATOMS = 30413

  End of Input File Reached
=================================================================