Subject: Alchemy 2000 MM3 energy

From: "Adel Abbas Ali Elazhary Sci. College" <[email-masked]>
Date: Mon, 14 Oct 2002 11:43:08 -0300 (GMT)

Dear CCL netters:

I am doing a conformational search using the alchemy 2000 program and I
do MM3 geometry optimization of each predicted conformation. I
found that the MM3 energy value of the optimized conformations is not
consistent. I mean after doing MM3 geometry optimzation energy of say 10
conformations and recalculating them again it is not ncessary to get the
same MM3 energy value. Since my molecule has a ring of about 20 atoms I
did the calculations for a similar smaller ring system and I found that
the energy values are consistent which means that the problem is with my
molecule only. I printed the output file with different MM3 energy values
for the same conformation and I noticed that there is a difference of
0.00001 A in the coordinates of some atoms and a difference of 0.0002 in
the initial steric energy values and after the geometry optimization each
output has a different route with quite different final energy and
geometry. I would greatly appreciate it if some one noticed this before
and know a solution to this problem to inform me. Thank you very much in
advance.

Best regards,

Adel El-azhary