Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11

From: Damodaran, Komath <Komath.Damodaran.elan.com>
Date: Thu, 7 Jun 2012 09:09:16 -0700

Hi Bill,

Thanks for your suggestion. In fact, I had compared the mdout files from
both runs and

whatever input variables that sander spits out at the beginning of mdout
of both runs do match.

That's why I felt like I had come to a dead end!

 

Thanks again,

Dam

 

>As far as I can remember, I do not recall any changes in default PB

>parameters within MMPBSA.py. However, the defaults in the pbsa routines

>called by sander may have changed between versions. You should be able
to

>check the mdout files produced by MMPBSA.py. Prior to the energy

>calculations, the mdout file should contain a list of all the input

>variables used for the sander calculation. If you compare the output
files

>from sander in Amber 10 and Amber 11, any differences should be the
cause

>of any discrepancies you see in the results. And since EPB is the only

>value that is different, you should only have to compare the PB input

>variables listed in those files.

>I hope that helps.

 

>-Bill

 

 

>On Wed, Jun 6, 2012 at 11:18 AM, Damodaran, Komath <

>Komath.Damodaran.elan.com> wrote:

>> Hi,

>>

>> I have a puzzle with MMPBSA calculations using Sander in Amber10 and

>> Amber11 versions.

>> I am running MMPBSA calculations on a moderate size protein:ligand

>> complex (about 300AAs).

>> When I use the same topology, trajectory and inpcrd files along with

>> the same mdinp options, the EPB value is lower in Amber 10 by about

>> 12kcal/mol. All other numbers (vdw, Coulomb term, cavity term) match

>> between Amber 10 and Amber 11.

>> I am wondering if any of the default parameters have changed between

>> versions 10 and 11.

>> Here are the input options that I use.

>

>> &cntrl

>>

>> nsnb=99999, ntb=0, cut=999.000000, imin=5,igb=10,

>>

>> /

>>

>> &pb

>>

>> sprob=1.400000, maxitn=1000, fillratio=4.000000

>>

>> radiopt=0, npopt=1, dbfopt=1, cavity_surften=0.005240,

>>

>> /

>>

>> END

>>

 


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Received on Thu Jun 07 2012 - 09:30:03 PDT
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