AMBER Archive (2006)

Subject: AMBER: problem with pattern searching in mm_pbsa_calceneent.pm, Amber8, when salt>0 using delphi version 4

From: Lwin, ThuZar (ThuZar.Lwin_at_stjude.org)
Date: Wed Jun 28 2006 - 19:58:14 CDT

Dear Amber community,

    

      I processed mm_pbsa script to obtain the stability free energy on
a single snapshot of a protein.

PROC 1

REFE 0

INDI 1.0

EXDI 80.0

SCALE 1.0

LINIT 800

MAXC 0.001

PRBRAD 1.4

SALT 0.5

FOCUS 0

PERFIL 80.0

SURFTEN 0.00542

SURFOFF 0.92

 

When SALT>0, mm_pbsa produce 2 delphi output files: one setting SALT=0
and another SALT=0.5.

I realized that the the statistics.out file produce PBCAL (-3109
kcal/mol) only based on "the corrected reaction field energy" from
SALT=0 delphi_output file.

total grid energy : 43269.43 kt

 self-reaction field energy : 1.2549232E-03 kt

 total s.charge,no epsin carrying : 11.8804

 corrected reaction field energy: -5214.351 kt

 total reaction field energy : -5214.350 kt

 

But Delphi_output file with SALT=0.5 produces

total grid energy : 43245.15 kt

 self-reaction field energy : 1.2549232E-03 kt

 total s.charge,no epsin carrying : 11.8806

 corrected reaction field energy: -5215.589 kt

 total reaction field energy : -5215.588 kt

 

In mm_pbsa_calceneent.pm file, when $multruns==2, it searches the line :
"total energy (including grid energy)" as follows:

if($multruns == 2 && $line =~ /total energy \(including grid energy\):
+(-?\d+\.\d+)/){

# solv = solv(SALT = 0.0) + total(SALT > 0.0) - total(SALT = 0.0)

          # delphi run 1 delphi run 2 delphi run 1

          if($j == 0){

            $solv -= $1;

          }

          else{

            $solv += $1;

          }

        }

 

However, the ouput file of Delphi version 4 does not produce the term
"total energy (including grid energy)"

 

Therefore when I substitute the "total energy (including grid energy)"
with "total grid energy" as follows:

if($multruns == 2 && $line =~ /total grid energy :
+(-?\d+\.\d+)/){

          # solv = solv(SALT = 0.0) + total(SALT > 0.0) - total(SALT =
0.0)

          # delphi run 1 delphi run 2 delphi run 1

          if($j == 0){

            $solv -= $1;

          }

          else{

            $solv += $1;

          }

        }

The PBCAL term (3122 kcal/mol) in statistics.out file seems to have
incorporated the salt effect by doing "solv(SALT = 0.0) + total(SALT >
0.0) - total(SALT = 0.0)". Please let me know if my approach is
correct.

 

Thanks,

ThuZar

 

 

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