Re: [AMBER] loadmol2 Segmentation fault

From: FyD <>
Date: Tue, 13 Apr 2010 20:25:51 +0200

Dear Dr Case,

>> - Why the three "F" do not have the same charge value ? My feeling is
>> that these three F are chemically equivalent, so their charge value
>> should be equivalenced.
>> - Why the two methylene groups of the cyclopropane group are not
>> chemically equivalent ? once again, my understanding is that the
>> corresponding charge values should be equivalent.
> These are AM1-BCC charges; with the algorithm in antechamber equivalent atoms
> do not necessarily have the same charges.

Thank you for your answer.

If we look at the corresponding FF library available .: we find
the AM1-BCC charge values for these 3 "F" (& others):
  "F1" "f" 0 1 131072 2 9 -0.231400
  "F2" "f" 0 1 131072 3 9 -0.221400
  "F3" "f" 0 1 131072 4 9 -0.216800

If I well understood this tuto., this FF lib is used in the prmtop
file generation .
  -4.21664022E+00 -4.03441722E+00 -3.95059464E+00 [...]

In the following paper: Bayly et al. J. Phys. Chem. 1993,97, 10269-10280.
It is written page 10271, just before the "Methods" section:

"In force-field treatments of conformationally labile species, it is
of course necessary to have identical charges on nuclei equivalent
with respect to the force field in terms of conformational
interconversion; e.g. all the hydrogens on a methyl group must bear
the same charge because otherwise the three degenerate rotamers of the
methyl would give rise to different energies." etc...

Why charge equivalencing is not introduced in this case for chemically
equivalent atoms ?

Thank you, regards, Francois

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Received on Tue Apr 13 2010 - 11:30:05 PDT
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