AMBER Archive (2009)

Subject: Re: [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10

From: Ray Luo (
Date: Thu Mar 26 2009 - 18:54:17 CDT

Hi All,

I'm sorry I didn't email the list on this. Dr. Gohlker's revised perl
scripts and many new examples (for the hybrid mmpbsa) have been
packaged in an Amber10 bugfix (17). You can download and try it out.
All reported problems on the list are gone after the fix in our tests.

All the best,

On Thu, Mar 26, 2009 at 4:44 PM, Daniel Oehme <> wrote:
> Hi all,
> Recently I have been getting some direct emails in relation to the
> modifications I made to the perl scripts for MM-PBSA in relation to
> the error I was getting for the "No data for 0+0 PB ELRAELE 0" error.
> I did get some feedback from Dr Gohlke's lab stating that
> modifications I made are acceptable.
> Also in their response it was mentioned that they would make some
> changes to the examples and the mm_pbsa_statistics script as soon as
> possible to clear up these issues. I am not sure if this is happening
> but I thought I would let everyone know that they can edit the files
> themselves and get MM-PBSA in AMBER 10 to run properly.
> Daniel Oehme
> PhD student
> La Trobe University
> On Mon, Jun 23, 2008 at 4:07 PM, Daniel Oehme <> wrote:
>> 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 files in the Examples directory have
>> the the AMBER9 format not AMBER10. The 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 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
>> I edited 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 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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