AMBER Archive (2009)

Subject: [AMBER] problem with energy calculations

From: Thomas Lake (thomas.lake08_at_imperial.ac.uk)
Date: Fri Jul 10 2009 - 11:13:55 CDT

Hello,

I have been modelling a peptide and am trying to carry out energy
calculations of it in the gas-phase. For this I use the mm_pbsa script,
but using only MM.

I am able to calculate the energy of just the peptide. However when I
include counterions (but no solvent), I get an error message:

'The system has extended beyond the extent of virtual box'

If I do reimaging of the trajectory (image center familiar) then I dont
get this error message. However the energies that are calculated give
very high vdW energies for certain frames. This I think is because
counterions have come into close contact in these frames.

I cannot think of any more possible solutions for this, so wandering if
anyone help me.

Regards

Thomas Lake
Imperial College London

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