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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Received on Sun Jul 02 2006 - 06:07:09 PDT
