AMBER Archive (2009)

Subject: [AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script

From: Samuel Genheden (samuel.genheden_at_gmail.com)
Date: Tue Jun 09 2009 - 07:43:19 CDT

Hello

I had trouble with the igb=5 and igb=7 options in MM/GBSA calculations
and after some time I found a strange thing in the
mm_pbsa_createinput.pm script.
This is the following code-snippet, from the create_sander_input subroutine:

if($igb == 1 || $igb == 2){
  $offset = 0.09;
}
else{
  $offset = 0.00;
}

Why should the offset be any different between, e.g. igb=2 and igb=5?
I cannot find any explanation either in the Amber 10 manual or the
original articles of igb=2/5 or igb=7. In my opinion, this is bug. I
obtain much more stable, precise and accurate result when I changed
the code so that the offset is 0.09 for all of the GB-methods. The
code is the same in Amber 8, 9 and 10.

Best regards,
Samuel

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