AMBER Archive (2008)

Subject: AMBER: mmpbsa INSTRNG error?

From: Sergio Wong (swong_at_mccammon.ucsd.edu)
Date: Sun Mar 09 2008 - 00:06:44 CST

Dear Amber users;

     I'm trying to perform an MMPBSA calculation using the mm_pbsa.pl
script. The ionic strength is set to 50 mM in my input script, yet the
pbsa.in file produced by the mm_pbsa.pl script writes:

istrng = 0,

      After tracking this down it comes down to lines 395 to 400 in the
mm_pbsa_createinput.pm file:

   if(exists $r_del->{"SALT"}){
      $istrng = $r_del->{"SALT"};
   }
   else{
     $istrng = 0.0;
   }
It never finds a "SALT" key, so istrng is always 0. By looking into the
mm_pbsa_input.pm file, it seems like the key should be "ISTRNG" instead of
"SALT". So, if I rewrite this, I get what I think is the desired input in
the pbsa.in file. Is this correct? or is the orignal code correct?

Thanks;

-Sergio
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