AMBER Archive (2005)

Subject: AMBER: ANAL module/AMBER8

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Tue Mar 22 2005 - 11:32:06 CST

I am using the ANAL module distributed with Amber8. I want to get a residue
based partitioned binding energy (vdWalls and Electrostatic) for a protein
bound to a non-covalent inhibitor. The following input is used:

    1 0 0 0 135 1
    0 0.0 0.0 0.0 0.0
    1 0 1 0 50 0
   15. 2.0 1.2 4.0
    1 20.0 20.0 20.0 20.0 20.0 20.0 20.0 20.0 20.0
ENERGY
System
RES -1 355
END
END
STOP
EOF

This way 355 th is the Inhibitor residue and in amber 4 version this worked
pefectly by giving a huge .outa file with all the required info. But this
time with Amber8 it seems to not work properly and gives sort of following
output which is very vague...

          INDIVIDUAL GROUPS INTERACTION

     GROUP INTRA INTER TOTAL

         1 0.00 0.00 0.00
         2 0.00 0.00 0.00

     TOTAL 0.00 0.00 0.00

          TOTAL INTERACTION ENERGY MATRIX

            1 2
    1 0.000 0.000
    2 0.000 703.331

          INDIVIDUAL GROUPS INTERACTION

     GROUP INTRA INTER TOTAL

         1 0.00 0.00 0.00
         2 703.33 0.00 703.33

     TOTAL 703.33 0.00 703.33

What could be the problem....
Thanks
Vineet

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