AMBER Archive (2009)

Subject: Re: [AMBER] binding energy

• Previous message: Simon Becker: "[AMBER] binding energy"
• In reply to: Simon Becker: "[AMBER] binding energy"
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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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• Previous message: Simon Becker: "[AMBER] binding energy"
• In reply to: Simon Becker: "[AMBER] binding energy"
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