AMBER Archive (2007)

Subject: AMBER: anal calculation error

From: gurpreet singh (gps.iitm_at_gmail.com)
Date: Tue Oct 16 2007 - 12:07:20 CDT

Hello Amber Users

I am using Amber 9 for my anal interaction energies calculations

I want to Calculate the interaction energy between a water molecule and a
monomer of a homo dimeric protein.
 I used the following input file

  1 0 0 0 0 1
   0 0.0 0.0 0.0 0.0
   7 0 0 0 0 0
 99.0 2.0 1.2 1.0
   1 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0
ENERGY
 first residue
RES 1 50
....................................................................................
which correponds to one monomer
END
 second residue (or group of atoms)
RES 200
.........................................................................................
water molecule
END
END
STOP

These dotted line is just for representation only

NOw the output file which i got from this shows the interaction energy as
follows :

          TOTAL INTERACTION ENERGY MATRIX

            1 2 3
    1 -2813.486 -0.463 -457.911
    2 -0.463 0.000 -17.139
    3 -457.911 -17.139 -3101.484

          INDIVIDUAL GROUPS INTERACTION

     GROUP INTRA INTER TOTAL

         1 -2813.49 -458.37 -3271.86
         2 0.00 -17.60 -17.60
         3 -3101.48 -475.05 -3576.53

     TOTAL -5914.97 -475.51 -6390.48

Few days back I got an answer from the archive that group 3 in the
interaction matrix corresponds to the left up residues which i did not
mention in the input file
So if that is the case than the interaction energies between the group 3 & 1
and group 2 & 1 should be same in this particular case or even if difference
will be there it should not be suc h high value since I am calculating the
interaction of water with the monomer of a homodimer so with respect to
other also the energy should be almost (if not exactly) similar.

Please suggest me something
what is group 3 actually if I am wrong or if not what else could be the
reason for the descripency.

Note : cut off is not all responsible I have checked at different cut off
values The value I am getting is always same

Waiting for your reply

Thanks & Regards
Gurpreet

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