On Mon, Feb 25, 2013 at 2:57 AM, <eneas.usal.es> wrote:
>
> Hi everyone,
>
> I performed a MD simulation of a protein-ligand complex through NAMD,
> obtaining a .dcd file. I´ve carefully read howto obtain MM-PBSA
> interaction energies both in the manual and the tutorials, but i´ve still
> have a problem.
>
> Apparently, MMPBSA.py does not recognized the .dcd files, and i´ve
> converted it to .crd.
MMPBSA.py should recognize DCD files. In fact, it uses cpptraj in order to
generate the temporary trajectory files that it analyzes, so if it works
with cpptraj it should work with MMPBSA.py.
> Prmtop files were properly splitted with cpptraj (For
> some reason antemmpbsa does not remove the adequate Flag Mass sections of
> the masks).
Do you get an error message with this? I'm not sure what this means. If
you are using AmberTools 12, there is an ante-MMPBSA.py test in
$AMBERHOME/AmberTools/test/mmpbsa_py/EstRAL_Files/ that works just fine...
(If you are using AmberTools 1.5, then you should upgrade to 12 before
using ante-MMPBSA.py).
> Nevertheless, when i´ve run MMPBSA.py an error related to box
> coordinates appear.
Error message? I'm guessing this is actually a cpptraj error message
(since MMPBSA.py never checks anything like this itself). It is worth
considering what went wrong.
> Again i´ve checked the forum for solutions and i´ve
> tried to save the trajectory as crdbox. Again, this doesn´t work too...
>
> So, i´ve decided to split the trajectory accordingly with the coordinates
> of the receptor, ligand and no solvated complex into 3 crd files. Each one
> was then splitted into the x number of the total frames of the simulation,
> leading to x .crd files per trajectory. Then i´ve run PBSA(single point)
> and obtained VdW, EEL and PBS interaction terms. I´ve calculated the
> average of each term and molecule and the substracted to obtained the
> final interaction energies, which typicallyis E=Ecomplex-Ereceptor-Eligand
>
> My question is if this method is the same as MMPBSA.py, if not please i´ll
> apreciate any answers.
>
Granted that you're generating all systems from a single trajectory, this
is the same thing. This is exactly what MMPBSA.py is supposed to automate,
although it adds a layer of protective error checking.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Feb 25 2013 - 05:00:05 PST
