Hi,
> with the risk of someone screaming "rtfm!" at me: is there a program
> that allows me to calculate the binding energy directly from a pdb-file?
Amber will require you to built prmtop and rst files, however this could
be easily scripted for a pure protein/peptide system. Your looking at not
much more than
Foreach X in <pdb structure-files> do
xleap <<EOF
source leaprc.ff99SB
foo = load $X
saveamberparm $X $X.prm $X.rst
quit
EOF
done
If you want to get around MMPBSA, then you could run just a onestep sander
minimization on each structure, i.e. using
&cntrl
imin=1, maxcyc=1, igb=1,
&end
or so as input each time. Then grep ETOT from your output file and
subtract E(protein)+E(Peptide) from E(complex). Binding free energies
calculated in this way, while not predictive or of any scientific value,
can at least be generated very quickly...
Regards,
Thomas
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri Oct 16 2009 - 04:30:03 PDT
