---------- Forwarded message ----------
Date: Tue, 03 Dec 2002 15:42:55 -0600
From: Numan Oezguen <numan_at_bohr.utmb.edu>
To: amber_at_heimdal.compchem.ucsf.edu
Subject: Energy decomposition with ANAL
Dear all,
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.
I appreciate your help and advise.
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
=================================================================
Received on Tue Dec 03 2002 - 14:58:05 PST
