AMBER Archive (2009)

Subject: [AMBER] Problem with MM-PBSA energy calculation

From: Rubben Torella (rubben.torella_at_gmail.com)
Date: Mon May 25 2009 - 10:58:41 CDT

Hi Amber users,
I'm trying to calculate the binding free energy between a protein and a
molecule.
I have performed MD simulations, then I have picked the last snapshot from
the MD simulation, I have stripped the water molecules and the counter-ions
from it as explained in the tutorial, and I have built the parmtop of the
ligand, receptor and complex, simply cutting from the pdb the coordinates of
the atoms and then using xleap. Then I use the script in the example folder
of mm_pbsa in order to create the snapshots of the complex, receptor and
ligand.
This script create the snapshot, I think correctly, but when I want to
calculate the free energy of binding using the script of binding in the
example folder, no output is created because of problem on the calculation
of the energy...
Here is my .log file errors:
 WARNING: Missing BOND for MM in 0 -> Taken from -1
    WARNING: Missing VDWNB for MM in 0 -> Taken from -1
I have this warning for every snapshot.. and finally no calculation has been
done.
I don't know where is (are) my error (s)...
Thank you in advance for every answer...
Best regards
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