AMBER: QM-MM output interpretation

From: Francesco Pietra <>
Date: Mon, 30 Jul 2007 07:08:36 -0700 (PDT)

I have carried out QM-MM for two non-polymeric 98-atoms (C, H, N, O) conformers
in the charge field of TIP3PBOX water. prmtop and inpcrd from antechamber. All
settings as in Tutorial A2 (may be a comma is lacking in; more
importantly I have set [qmask=':1'] because it is a single residue.

The structures (mdcrd) are OK, except for poor performance in dealing with the
conformation of highly conjugated (non aromatic) cyclic systems, as expected
for PM3 and all other semiempiricals.

I am unsure how to read the outputs. As to relative populations of the two
conformers, I refer to EPtot from last NSTEP (1000) (correct?). If so:

Conformer 1(eq):
PM3ESCF = -239.3042 (RMS fluctuations 13.0877; Ewald errors estimate at NSTEP
1000 = 0.3610E-01, at RMS = 0.2741E-02) [I assume these are kcal/mol, though
irrelevant to present comparison; at any event, where to find a table of units
in use in Amber9?]

Conformer 2(ax):
PM3ESCF= -252.2996 (RMS fluctuation 8.6619; Ewald error estimate at NSTEP 1000
= 0.3687E-01, at RMS 0.2049E-02)

At this understanding of reading the outputs,I can't reach any conclusion as to
the relative populations.


francesco pietra

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Received on Wed Aug 01 2007 - 06:07:22 PDT
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