AMBER Archive (2005)

Subject: AMBER: Anal - problems with energy analysis

From: Yogesh Sabnis (ysabnis_at_yahoo.com)
Date: Tue Jul 12 2005 - 03:33:30 CDT

Dear Amber users,

I am trying to use Anal in Amber8 to calculate the
interaction energies between each residue in the
protein. The ligand is the 199th residue. But, it does
not seem to work.

Here is my anal.in file:
Calculate the interaction energies between each
residue (ligand, water)
1 0 0 0 0 1
0 0.0 0.0 0.0 0.0
1 0 1 0 50 0
15.0 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
END
interaction energy analysis
RES -1 199
END
END
STOP

anal.aout file:
                                                      
                         
          NUMBER OF ATOMS = 3521

          loading the groups for analysis

    ----- READING GROUP 1; TITLE:
 interaction energy analysis
                      
      ***PROBLEMS WITH GROUPRES -1 199 0 0
 0 0 0 0 0 0 0 0 0 0*******

      Number of atoms in this group = 0
    ----- END OF GROUP READ -----
..............
..............
..............
..............
INDIVIDUAL GROUPS INTERACTION

     GROUP INTRA INTER TOTAL

         1 0.00 0.00 0.00
         2 2317.10 0.00 2317.10

     TOTAL 2317.10 0.00 2317.10

I am not sure why it is giving me just 2 groups? Which
groups are they?

I would appreciate any help regarding this issue.

Thank you.

Kind regards,

Yogesh

########################

Yogesh Sabnis, PhD

BMC, Box 574,

Avd Org. Farm. Kemi,

Husargatan 3,

Uppsala - 751 23

Sweden

__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu