Hi all,
I have question regarding the optimal parameters
values when one using APBS/sander.APBS via MMPBSA.py or MMPBSA.pl
interface.
My guess is that in such a case perhaps the APBS defaults
( which are reported e.g. here
http://mccammon.ucsd.edu/iapbs/usersguide/using-amber.html#AEN187 )
are the best choice to get the most accurate overall solvation energies
using this module.
However these defaults differ a bit from those of Amber PB.
For example:
Internal dielectric constant:
Amber default = 1, APBS default = 2
External dielectric constant:
Amber default = 80, APBS default = 78.4
Cavity surface tension :
Amber defaults:
0.0378 kcal/mol/A^2 (for INP = 2 and RADIOPT = 1)
0.00542 kcal/mol/A^2 (for INP = 1 and RADIOPT = 0)
APBS default = 0.0251 kcal/mol/A^2
(It seems that APBS module is compatible actually just with RADIOPT = 0 )
so here we have quite a big difference 0.00542 versus 0.0251.
so to be sure I am just asking this question, also to learn about
another important parameters which should be eventually changed
from the Amber defaults to APBS ones (if any).
I would like also notice probable error in translating ISTRNG parameter
into
APBS parameter "ionc".
In case of PB section of the mm_pbsa.in file (input file for PERL version),
there is explicitly stated that the ISTRNG parameter is in mM units which
e.g. means that the
right value for the physiological ionic strength of Na+,Cl- ions is 150
here.
However when translated for the sander.APBS (in &apbs section) it should
be perhaps converted
to APBS native units for this parameter (here "ionc") which is in molar
(M) units.
So having in PB section "ISTRNG=150", for sander.APBS it should be
translated
(written in &apbs section) as "ionc=0.15, 0.15" not "ionc=150,150" as it
is doing now
(Amber12/AT13 fully patched)).
In case of MMPBSA.py there is "istrng" value also just simply copied into
"ionc"
parameter, but here it is OK because here "istrng" is in M units so no
"value-conversion"
is necessary.
Thanks in advance for any comments to this topic.
Best wishes,
Marek
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Tue May 07 2013 - 12:00:03 PDT
