Hi All
I am using the openbabel command line for generating 3D conformer for s set
of mol2 molecule database, and then use the database for a virtual
screening. i made a shell by the following commands:
#! /bin/bash
for f in *.mol2; do
obminimize -ff Ghemical -n 10000 $f (minimize the energy by Ghemical force
field, set up 10000 as max steps)
obconformer 50 1000 $f >Meg/$f (generate best of conformer out of 50 after
1000 geometry optimization steps, and save in fold Meg with same file name)
done
this question is that after this process, the result is totally difference
with the results of another software named Avogadro (use the same Ghemical
force field for energy minimization).
i want to figure out how the difference came out? should they be same since
their use same force field for calculation?
Mac
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