Dear Amberists,
I've been having some hard times making MMPBSA.py understand what is it that
I want to do.
I'm using it to estimate binding free energy between an enzyme and a ligand,
pretty standard
stuff. In order to do so, I am using several trajectories in the expectation
that by doing so I
will better sample phase space and therefore will obtain more statistically
meaningful results.
However, when I tell MMPBSA.py that I want it to cut through the
trajectories from frame 200
to frame 20000 it will tell me this:
WARNING in safe_close(): Attempting to close a NULL FILE and buffer!
Beginning quasi-harmonic entropy calculation with ptraj...
Error! Ptraj failed. Check coordinate and topology files for the complex.
And when I start from frame 1 to frame 20000 it will go on and give me my
calculations, except
that it will take a single frame from each trajectory. Does anyone have a
clue of what on earth is
going on here? At first I thought it was something to do with the
trajectories being too short, maybe
a bug. But the interval is valid for all trajectories.
Looking forward to your assistance.
Gabriel
---------
Graduation student at Federal University of Paraíba, Brazil.
LQQC - Laboratory of Computational Quantum Chemistry
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Received on Wed Apr 27 2011 - 05:00:06 PDT
