[AMBER] No VDWAALS EEL in PB MMPBSA.py job

From: JPB <jpb.q4md-forcefieldtools.org>
Date: Fri, 27 Jun 2014 17:27:25 +0200

Dear users,

I am performing free energy calculation with MMPBSA.py.
In one system with the Poisson Boltzmann model,
the van der Waals energy (VDWAALS) and the electrostatic
energy (EEL) are not taken into account.
In the FINAL_RESULTS_MMPBSA.dat file the lines devoted to
VDWAALS and EEL do not appear and it is also surprising
that for the ENPOLAR contribution "Std. Dev."
and "Sd. Err. of Mean" equal 0.00

In the _MMPBSA_complex_pb.mdout.i files, one can read:
                eff.c(2829) enb --> 0.000
                eff.c(2830) eel --> 0.000
                eff.c(2831) e_pb --> 0.000

In the meantime in the same job these two contributions are computed
when using the generalized Born model.

It seems that something somewhere turns off the computation of electrostatic
and van der Waals energies.
My system is an oligomer made of 12 molecular units.
I performed the same computations with oligomers of 1, 2, 4, 6, and 9
molecular units and these two contributions were computed.
I don't know where to look for the origin of this problem with the
12-unit system.
Any help is welcome.

Cheers.
JPB.



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Received on Fri Jun 27 2014 - 08:30:02 PDT
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