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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Received on Wed Jun 10 2009 - 01:08:16 PDT
