AMBER Archive (2007)

Subject: Re: AMBER: antechamber/charges/conformation

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Jun 11 2007 - 03:40:11 CDT

Quoting Francesco Pietra <chiendarret_at_yahoo.com>:

> 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.

When you do a conformational search, the H-bonds available in your
'big' molecule will be important driven forces for defining your
minimum. This might not what you wish...

> (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?

Usually you cut your molecules into fragments "that make sense"...
See for instance Cieplak et al. J. Comput. Chem., 1995, 16, 1357-1377.

You have examples of fragment building in the Tutorial available @
http://q4md-forcefieldtools.org/Tutorial/

We are about to release in R.E.DD.B. many complex force field topology
databases generated by R.E.D. III and IV beta. Check R.E.DD.B. & you
should find examples of fragment building.

regards, Francois

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu