AMBER Archive (2003)

Subject: ANAL in AMBER

From: A.Madhumalar (malar_at_mbu.iisc.ernet.in)
Date: Tue May 06 2003 - 02:25:05 CDT

Dear amber users,
  I am trying to calculate energy of a nucleotide using ANAL module of
amber, for that i have defined three groups phospate group alone, other
sugar backbone atoms and base atoms.In the anal output, for phosphate
group,the matrix looks as
 
   ENERGY CONTRIBUTION BY GROUPS

     GROUP BOND ANGLE DIHEDRAL VDW14 EEL14 VDWNB
EELNB HBOND CONSTRAINT TOTAL

       1 2.71 0.83 1.28 0.46 20.83 -1.76
15.57 0.00 0.00 39.922

but in the other matrices

 VDW (N-B + 1-4) INTERACTION ENERGY MATRIX
 it is 0.00

     1 2 3

  1 0.000 -0.355 -0.575

ELECTROSTATIC (N-B + 1-4) INTERACTION ENERGY MATRIX
 
        1 2 3
   
1 0.000 -13.975 2.652

1 group defined is phosphate group, its VDW & EEL energy value is 0.00 in
the component matrices, but it is nonzero in energy contribution by
groups. can anyone tell me where i am wrong? How it is calculated? Thanks
for any suggestion.

Madhu