AMBER Archive (2005)

Subject: Re: AMBER: (no subject)

From: Thomas Cheatham (cheatham_at_chpc.utah.edu)
Date: Fri Dec 23 2005 - 15:37:57 CST

> I am a new beginner of Amber package (Amber8), I have
> some difficulties to assign the charges in general
> organic molecules.

To better understand how the force fields were developed and how to use
AMBER, it is beneficial to go through the tutorials,

        http://amber.scripps.edu/tutorial/index.html

and in particular look at the Beginning AMBER workshop link and tutorials
4 and 5. This only indirectly specifies how to develop a new residue, but
it definately a useful pre-requistite.

> I want to build Sodium undecyl L-alanine Leucine. I
> can draw the undecyl part in Xleap, then add to the
> sequence of Ala & Leu, but there is no charge for the
> atom in the undecyl part. I used Antechamer to
> generate the undecyl-Ala-Leu with -1 charge to get the
> atomtype and charge. I found the whole system had -1

Antechamber alone will not calculate charges unless you run Mopac (or an
appropriate Divcon version) with AM1-BCC charges or supply an optimized
geometry from a Gaussian calculation for RESP.

Unlike the atom types used for specifying bond, angle and dihedral
parameters (and van der Waals interaction), charges are not typically
transferable from one molecule to the next. Although a CT-CT (carbon
tetrahedral bond) is virtually the same in ethane, propane or cyclohexane,
the charges on the carbon will depend on its molecular environment. How
one determines this charge differs from force field to force field. For
the CHARMM all27 force field and related, a complicated procedure of
optimization of the isolated molecule with some surrounding water fitting
interaction energies is applied; see Professor Alex MacKerell's force
field resources at:

   http://www.pharmacy.umaryland.edu/faculty/amackere/param/force_field_dev.htm

For the Cornell et al. force field, QM calculations at the 6-31G* level
are applied to optimize geomtries and get Merz-Kollman electrostatic
potentials which are fit, with restraints to prevent large charges on
buried atoms, with the RESP procedure (using Antechamber and reading in a
Gaussian log file). If you use Gaussian, the input options look like:

# opt hf/6-31g(d) geom=connectivity scf=tight pop=mk iop(6/33=2,6/42=6)

The RED package (see link on main AMBER www page at amber.scripps.edu) can
facilitate doing this consistently with Gaussian, GAMESS and other QM
programs. If you need a quick estimate, the AM1-BCC charges can be used.
A variety of papers in the literature discuss all of this (search for
papers by Cieplak, P. ; Bayly, C. ; Cornell, W.D. ; Dupradeau, F.-Y.;
etc).

Good luck with your force field developments and if all goes well with
your new parameters, consider contributing them to the public at the
AMBER Parameter Database:

        http://pharmacy.man.ac.uk/amber/

Happy Holidays to all,

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham

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