> 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
Received on Thu Sep 21 2000 - 07:02:16 PDT
