AMBER Archive (2009)

Subject: RE: [AMBER] Error in binding energy (MM PBSA)

From: Ray Luo (
Date: Fri May 08 2009 - 11:42:58 CDT


Could you take a look of your snapshots in VMD? There might be mismatches
between your prmtop files and inpcrd files for mmpbsa calculations. You can
easily spot this if the structures are not displayed correctly.

All the best,

Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email:
Phones: (949) 824-9528, 9562

-----Original Message-----
From: [] On Behalf
Of Vikas Sharma
Sent: Thursday, May 07, 2009 11:43 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Error in binding energy (MM PBSA)

Dear Dr. Ray Luo

Thanks for the reply..
Actually i used antechamber (bcc charges for the ligand)...could this be the
Shall i use rersp charges n also do Gaussian calculations?

i checked the ligand inpcrd and prmtop files but couldnot understand...i am
pasting both the files below...if you could figure out the problem....
i am waiting for your suggestion

Thanks a lot

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