Dear all,
I have some elementary questions regarding setting of some parameters
in input file for mm_pbsa calculation.
#1
In some older contribution in mailing list
http://archive.ambermd.org/200911/0159.html
was suggested to set
SURFTEN 0.0072
SURFOFF 0.00
for GB calculation ( .GB section ) and
SURFTEN 0.00542
SURFOFF 0.92
in case of PB calculation ( .PB section ) - having INP=1 (this values are
also recommended directly in the *.in file)
My questions are:
a)
Why in MM_PBSA tutorial:
http://ambermd.org/tutorials/advanced/tutorial3/section3.htm
in .PB section is set:
SURFTEN 0.0072
SURFOFF 0.00
if this should be reasonable setting just for GB calculation ?
b)
In example file
$AMBERHOME/src/mm_pbsa/Examples/03_MMPBSA_Binding/mm_pbsa.in there
is this setting:
RADIOPT 1
INP 2
#
SURFTEN 0.04356
SURFOFF -1.008
Was here some reason for it ? I would assume here (in example file)
probably more common/frequent setting:
RADIOPT 0
INP 1
SURFTEN 0.00542
SURFOFF 0.92
#2
If one is calculating free energy of rec/lig binding dG using mm_pbsa.pl
and for calculation of solvent contributions
I used PB with setting:
RADIOPT 0
INP 1
SURFTEN 0.00542
SURFOFF 0.92
and for NN analyses I would like to use alternative IGB=1 ( .NM section
), is it OK to use
SURFTEN 0.0072 ? I think yes because this value is
recommended for GB calculation in .GB section so here probably should be
the same. I would like
just to ensure me... I would like also ensure my self that it is OK if I
use for calculation of free energy of binding combination of "dH"
particularly calculated with PB and "TdS" where GB was used ( GB=1 in .NM
section) instead distance-dependent dielectric.
Thanks in advance for any relevant comments !
Best wishes,
Marek
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Received on Mon Jan 31 2011 - 10:00:03 PST
