Re: [AMBER] Energy Decomposition using mmpbsa script

From: Bill Miller III <>
Date: Sat, 12 Mar 2011 08:31:16 -0500

If all the input variables are exactly the same, then and should give you the exact same answer for all components. We made
sure this was the case when we wrote and released The difference
is that some of the variables have different defaults in than the
suggested values in, such as igb.

What are the lines in and surrounding line 358 of
AMBER-10.0/amber10/lib/mm_pbsa/ ? Also, could you post
your input file for

And have you tried decomposition analysis with Did that give you
any problems?


On Sat, Mar 12, 2011 at 8:05 AM, Eliac Brown <> wrote:

> Dear AMBER
> Firstly, I calculated the mmgbsa binding energy using and using
>, I got the identical final delta energies, but the the energy
> components for each of ligand, receptor and complex were different using the
> two mmgbsa scripts, is that normal? (not I used MS=0 to force the program to
> calculate the solvation using LCPO method as it is done with pythone
> script).
> Secondly, I am trying to calculate the energy decomposition using GB model
> ( , if I specified PB = 0 it gives me an error :
> AMBER-10.0/amber10/lib/mm_pbsa/ line 358
> when I change PB to 1, it works normally, but I don't need to calculate PB
> where it is very expensive calculation. how can I do that?
> Thanks in advance for your help
> Eliac
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sat Mar 12 2011 - 06:00:03 PST
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