Re: Do I have to rerun 1ns MD??

From: Holger Gohlke <>
Date: Sun 22 Sep 2002 12:30:40 -0700

Dear Martin,

try "199-199" as input for your decomposition. Rerunning the MD job
should not be necessary then.

Best regards



I'd like to ask you for advice or opinion.

I've run a 1ns MD in explicit solvent of a protein-ligand complex to
describe the energetics of binding. Then, AMBER 7 MM-PBSA came to play
and showed the possibility of decomposing the binding energy by residue.
I'd be very happy to use it but as I've used a single-residue-ligand
topology for my MD, I gather that I cannot use MM-PBSA decomposition
(error message - Wrong format for decomp: 199) {199 is the ligand
residue number}.

Is there a way how to avoid rerunning the 3-week MD job and get the
decomposed energies?
I imagine sth like rearranging crd according to the new
multi-residue-ligand top file....

Thank you for your comments.

Best regards,


Martin Lepsik, PhD student Phone: +420/2/20183-540, Fax:
Dept. of Theor Chem & Center for Complex molecular Systems and
Institute of Organic Chemistry and Biochemistry (IOCB)
Flemingovo nam 2,
Czech Academy of Sciences,
166 10, Prague 6,
Czech Rep.


Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
Received on Sun Sep 22 2002 - 12:30:40 PDT
Custom Search