Dear Martin,
try "199-199" as input for your decomposition. Rerunning the MD job
should not be necessary then.
Best regards
Holger
>>>>>
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
------------------------------------------------------------------------------------------------------------------------------------------------------------
Martin Lepsik, PhD student Phone: +420/2/20183-540, Fax:
+420/2/20183-292
Dept. of Theor Chem & Center for Complex molecular Systems and
Biomolecules
Institute of Organic Chemistry and Biochemistry (IOCB)
Flemingovo nam 2,
Czech Academy of Sciences,
166 10, Prague 6,
Czech Rep.
URL: www.uochb.cas.cz/~teochem
<<<<<
--
+++++++++++++++++++++++++++++++++++++++++++++
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
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++
Received on Sun Sep 22 2002 - 12:30:40 PDT
