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.Prmtop files were properly splitted with cpptraj (For
some reason antemmpbsa does not remove the adequate Flag Mass sections of
the masks). Nevertheless, when i´ve run MMPBSA.py an error related to box
coordinates appear. 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.
Thanks a lot.
Carlos T. Nieto
_________________________________________________
Carlos T. Nieto
Organic Chemistry Department
University of Salamanca
Avda de los Caidos s/n
37008 Salamanca
SPAIN
T: 00 34 923294474
Fax: 00 34 923294574
email:eneas.usal.es
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Received on Mon Feb 25 2013 - 00:00:02 PST
