AMBER Archive (2008)

Subject: AMBER: MM-PBSA in AMBER 10

From: Daniel Oehme (oehmes4_at_gmail.com)
Date: Thu Jun 05 2008 - 00:27:39 CDT

Hi,

I have recently received a copy of AMBER 10 and have been running some
tests with the MM-PBSA suite of perl scripts. I have come across a
couple of issues while doing so.

The first is that the mm_pbsa.in files in the Examples directory have
the the AMBER9 format not AMBER10. The mm_pbsa.in in
$AMBERHOME/src/mm_pbsa/Examples is correct but the ones in the
01_GenerateSnapshots, 03_MMPBSA_Binding etc are of the old format.

Secondly, running the ras_raf 03_MMPBSA_Binding example did not work,
even when changes were made to mm_pbsa.in to align it with the AMBER10
format. The error I got was "No data for 0+0 PB ELRAELE 0". By
searching the perl scripts I was able find ELRAELE defined in
mm_pbsa_statistics.pm. I edited mm_pbsa_statistics.pm. such that the
$PB section of $VARREG (Lines 131-143) read:
           "PB" => {
                     "ELRAELE" => [0,0,'ELRAELE = +(-?\d+\.\d+)'], #
                     "EPB" => [0,0,'EPB = +(-?\d+\.\d+)'],
                     "PB" => [1,0,'corrected reaction field
energy: +(-?\d+\.\d+)'],
                     "PBDIS" => [1,0,'EDISPER = +(-?\d+\.\d+)'],
                     "PBCAV" => [1,0,'ECAVITY = +(\d+\.\d+)'],
                     "PBNONPOL" => [0,0,'ENPOLAR = +(\d+\.\d+)'],
                     "PBSUR" => [3,5],
                     "PBCAL" => [3,6],
                     "PBSOL" => [2,7,'+PB_PBCAL+PB_PBSUR+PB_PBDIS'],
                     "PBELE" => [2,8,'+PB_PBCAL+?MM_ELE'],
                     "PBTOT" => [2,9,'+PB_PBSOL+?MM_GAS']
                   },
By changing index 0 of ELRAELE, EPB, PBNONPOL to 0, MM-PBSA would
complete. Can anyone tell me if this was a valid way of solving the
problem or have I misunderstood something.

Finally, reading though the changes to mm_pbsa.in I noticed that the
Surften and Surfoff values have been changed from the values used in
AMBER9, to values which depend on the radii type used or if IVCAP is
set. My questions regarding this are first - have the values that have
been suggested for Surften/Surfoff been published anywhere. Secondly,
why are the AMBER9 values used for Surften and Surfoff in the GB
calculations section instead of the new values as given in the PB
section. I would think that the non polar solvation energy would be
independent of the implicit solvent method used and therefore the same
value for Surften/Surfoff should be used for both methods

Thanks in advance for any help I receive.

Daniel Oehme
PhD student
La Trobe University
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