AMBER Archive (2007)

Subject: AMBER: interaction energy calculations

From: gurpreet singh (gps.iitm_at_gmail.com)
Date: Tue Oct 09 2007 - 12:06:24 CDT

Hello Amber users

I am using Anal module for calculating the interaction energy between some
specific residues using the following input file

..............................................
   1 0 0 0 0 1
   0 0.0 0.0 0.0 0.0
   1 0 0 0 0 0
 99.0 2.0 1.2 1.0
   1 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0
ENERGY
 first residue
RES 50
END
 second residue (or group of atoms)
RES 146
END
END
STOP
......................................

In this file I am using two groups i,e RES 50 and RES 146 i.e I want the
interaction energy between these two groups but in the ouput file it is
showing total number of groups one more than the this ie 3 for this case
look at the output below

..................................................

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

            1 2 3
    1 5.369 -0.032 -4.946
    2 -0.032 5.388***********
    3 -4.946*********** 2064.981

          INDIVIDUAL GROUPS INTERACTION

     GROUP INTRA INTER TOTAL

         1 5.37 -4.98 0.39
         2 5.39**********************
         3 2064.98**********************

     TOTAL 2075.74**********************

          ELECTROSTATIC (N-B + 1-4) INTERACTION ENERGY MATRIX

            1 2 3
    1 5.177 0.121 -12.168
    2 0.121 5.188 -15.238
    3 -12.168 -15.238 -2340.130

          INDIVIDUAL GROUPS INTERACTION

     GROUP INTRA INTER TOTAL

         1 5.18 -12.05 -6.87
         2 5.19 -15.12 -9.93
         3 -2340.13 -27.41 -2367.53

     TOTAL -2329.76 -27.28 -2357.05

.......................................................................

So what is the exact significance of these groups here , how come they are 3

waiting for your reply

Gurpreet

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