On Wed, 2015-07-29 at 11:32 +0530, Shruti Koulgi wrote:
> Hello All,
> Is it possible to perform MM-GBSA calculations at temperatures other tahn
> 300 K using the MMPBSA.py executable.
No, I don't think so. Note that for MM/GBSA and MM/PBSA, the only place
in the equations where temperature is used is in the expression
accounting for a non-zero salt concentration. In this case, I believe a
temperature of 300 K is hard-coded in the GB. In sander (in AmberTools
15), lines 1081 to 1085 in mdread2.F90 read:
! ---------------------------------------------------------------------
! ---get Debye-Huckel kappa (A**-1) from salt concentration (M), assuming:
! T = 298.15, epsext=78.5,
kappa = sqrt( 0.10806d0 * saltcon )
So you can see there's really no way to adjust this for different
temperatures unless you change the code directly. Note that by default,
MMPBSA.py doesn't use sander, and that same conversion is done before
being sent to nab on line 295 of
$AMBERHOME/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 29 2015 - 07:30:03 PDT
