AMBER Archive (2006)

Subject: AMBER: ISTRNG or SALT in MM_PBSA

From: Qizhi Cui (qzcui_at_scripps.edu)
Date: Wed Dec 13 2006 - 21:23:48 CST

Hello,

According to AMBER9 manual, there is an ionic strength parameter, ISTRNG,
for PB solvent model used in the MM_PBSA input file. But from my recent
MM_PBSA calculations, I notice setting different ISTRNG values never take
any effect on the related output PB energy terms. I notice "istrng" in the
created pbsa.in file is always zero.

I looked at the source code, mm_pbsa_createinput.pm, and found that
$istrng actually points to parameter name "SALT" (see line 396:
$istrng=$r_del->{"SALT"}). So, I changed the parameter name "ISTRNG" to
"SALT" in the mm_pbsa input file. Now, "istrng" in pbsa.in is assigned
correct value (same as SALT) and has effects on the related PB energy
terms.

Does it mean the AMBER9 manual giving the wrong parameter name? (On page
270, ISTRNG in the @PB section of MM_PBSA input file should be changed to
SALT?)

Qizhi

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