On Tue, 2014-12-09 at 16:49 +0000, de Manzanos Guinot, Angela wrote:
> Hi,
>
> I have a system with multiple ligands. In order to calculate the
> MMGBSA for each ligand, MMGBSA.py calculates the complex contribution.
> However the complex is the same for all the ligands, so I was
> wondering if there is a way to avoid MMGBSA.py calculating the energy
> of the complex each time? This will save me a lot of time.
Oh, neat. No, this isn't currently possible, although it would be an
interesting feature to add, developer time permitting.
You can always do it by hand, though (as it seems you are thinking about
below).
>
> If not, is it reasonable to create a script that calculates the energy
> contribution of each snapshot by doing a single step minimization of
> the .rst of each snapshot (setting igb=2 or 5), extracting the
> different energy terms for each snapshot to calculate GGAS. And for
> the GSOLV extracting the EGB from the output files and then
> calculating the ESURF measuring the SASA with cpptraj and finally
> calculating ESUR=surften*SASA+saltcon to obtain GSOLV? I have the
> first bit already scripted, but I am not sure about the ESURF.
You can also use a trajectory and do a single-point calculation (by
doing a 1-step minimization) on each snapshot using "imin=5". This is
actually what MMPBSA.py does internally.
MMPBSA.py now uses cpptraj to either compute the "molsurf" or "LCPO"
surface area and does what you propose. So this is reasonable.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Dec 09 2014 - 09:30:02 PST
