AMBER Archive (2007)

Subject: AMBER: antechamber/charges/conformation

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sun Jun 10 2007 - 02:02:15 CDT

Three questions related to "charges computed are those
for the conformation you provide" (manual,
antechamber, p. 80, lines 2-3).

(1) I wonder what the expectation may be for a MD
conformational search of a large non-polymeric
molecule (i.e. no repeating units) starting
antechamber with an approximately minimized structure.
Approximately so, because MM programs do not allow a
preliminary systematic global conformational search
for so many degrees of freedom. Notice that, because
of chirality axes and fixed asymmetric centers
present, the different conformers are in a
diastereoisomeric relationship.

(2) Are the above prospects better if the large
molecule is first cut into fragments and the charges
computed from them? What about the reliability of the
dipole moment obtained this way? Notice that fragments
still contain movable dihedrals (it is unconceivable
to cut the molecules into such small fragments that do
not comprise dihedrals).

(3) Can "divide and conquer" be manually driven to cut
the molecules according to chemical intuition, i.e.,
can breaking bonds be manually selected?

Thanks
francesco pietra

       
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