AMBER Archive (2000)

Subject: Re: interaction energy

From: Michal Otyepka (otyepka_at_aix.upol.cz)
Date: Thu Sep 21 2000 - 09:02:16 CDT


> I'm trying to calculate the interaction energy between a drug molecule
> and the receptor over a MD trajectory. Can anyone tel me how I would go
> about obtaining this interaction energy?
>
> Chris Higgs

1, using CARNAL make a set of pdb or RST files

FILES_IN
        PARM p1 topology;
        STREAM s1
        trajectory;
FILES_OUT
        COORD c1 name RST;
DECLARE
OUTPUT
        COORD c1 s1;
END

2, using ANAL analyze energy interaction

Analysis of enzyme/inhibitor complex
    1 0 0 0 289 1
    1 X Y Z 90
    1 0 0 0 0 1
   10 2.0 1.2 1.0

ENERGY
...
END

I used for similar analysis a short shell script. Below you can find
example for inspiration.

#!/bin/csh

  anal -O -i decomp.in -o decomp.out -p topology -c start.RST.file
  rm -f t
  awk '{if (NR >= nr.A && NR < nr.B) print $2}' decomp.out > ts
  awk '{x = x $0 " "} END {print x }' ts > t
  rm ts
  
set j = 2 while ($j < nr.end)
  anal -O -i decomp.in -o decomp.out -p topology -c next.RTS.file.$j
  echo $j
  @ j++

#analyza vdw
  awk '{if (NR >= nr.A && NR < nr.B) print $2}' decomp.out > $j
  awk '{x = x $0 " "} END {print x }' $j > ts
  cat t ts > x
  rm ts t $j
  mv x t

end

where nr.A and nr.B are rows of your interest in the decomp.out file.

Good luck, Michal Otyepka

--------------------------------------------------------------
Department of Inorganic & Physical Chemistry
Palacky University, 771 46 Olomouc, Czech Republic
http://www.upol.cz/kafch