Marek,
Amber PBSA and APBS should give you the same energies, within
numerical accuracy, if you use the same parameters, such as dielectric
constants, radius definition, surface definition and tension etc. This
has nothing to do with which package you use. If you see different
energies, you are most likely using different parameters, i.e.
different default values.
Developers often set different default parameters for different
intended usages. In Amber/PBSA, we set these values for MMPBSA
applications. In APBS, these values are set for some other
applications. I believe you can find these in their user manual.
Ray
On Tue, May 7, 2013 at 11:27 AM, Marek Maly <marek.maly.ujep.cz> wrote:
> 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 - 15:00:02 PDT
