[AMBER] Fwd: high bidning energy MMPBSA

From: kamlesh sahu <kamleshsemail.gmail.com>
Date: Thu, 17 Jun 2010 10:51:11 +0900


sorry for the mistake. the second command I used was

$AMBERHOME/exe/mm_pbsa.pl binding_energy_Example.mmpbsa >


---------- Forwarded message ----------
From: kamlesh sahu <kamleshsemail.gmail.com>
Date: Thu, Jun 17, 2010 at 10:45 AM
Subject: high bidning energy MMPBSA
To: AMBER Mailing List <amber.ambermd.org>

Hi all,

I am running binding energy calculations using MMPBSA on amber 10.
Previously I was getting some error messages which were solved when I used
fillratio=4.0. Now I finished the calculation but the binding energy seems
abnormally high. First I extracted 20 snapshots using the command

$AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
then I run the command

$AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa_Example >
I get a binding energy of -37091150.59 kcal/mol. (please see attached
20-snaps_statistics.out and other input and log files)
Could somebody tell me what part of calculation I am possibly making mistake
in ?

Thank you

Kamlesh Kumar Sahu (post doc researcher)
Riken, wako, Saitama, JAPAN

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Received on Wed Jun 16 2010 - 19:00:06 PDT
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