Hi Jason,
Thank you very much, I have written a script that does it and I obtain very similar results than the ones I obtained previously with MMGBSA.py, only from the third decimals are a bit different which looks like rounding issues, but nothing significant (as the energy terms of the receptor and comples are arounf exp5). If I set igb5, the saltcon and surften appropriate for my system, extdiel=80.0 and gbsa=1 it calculates the ESURF using LCPO too, so I don't need an extra calculation with cpptraj. Also, regarding imin=5 it doesn't work as it gives an error regarding the .inpcrd, looking at the amber manual I found this:
IMPORTANT CAVEAT: The initial coordinates input file used (-c <inpcrd>) should be the
same as the initial coordinates input file used to generate the original trajectory. This is because
sander sets up parameters for PME from the box coordinates in the initial coordinates input file
And as I generate the individual trajectories by stripping things from the raw trajectory, I cannot obtain the initial inpcrd of these, I tried all sort of things here. Anyway, I solved the problem by doing a .rst from each snapshot of my trajectory to obtain the compelx, receptors and ligands and then doing a script that modifies sander input to do a single step minization of each rst. And modifying the output files accordingly to obtain the different energy terms for the calculation of MMGBSA.
Many thanks for your help,
Angela
________________________________________
De: Jason Swails [jason.swails.gmail.com]
Enviado: martes, 09 de diciembre de 2014 17:12
Para: amber.ambermd.org
Asunto: Re: [AMBER] Query about MMPBSA.py
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 Wed Dec 10 2014 - 02:30:03 PST
