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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Received on Sun Oct 21 2007 - 06:07:12 PDT
