On Thu, Mar 13, 2003, Marvin Rich wrote:
> I have been using the tip5p water model with amber6 and cvff, running both
> through InsightII software. I notice that the N-H - O (wat) hydrogen bond
> is less than the C=O -H(wat) hydrogen bond when using amber6 (with the
> tip5p model) in a simple dialanine water system. This is not the case
> when using amber6 with tip3p, or when the tip5p is implemented with the
> cvff forcefield.
>
> Has anyone used tip5p with amber5 or 6 and noticed these irregularites?
I'm assuming that "less than" above means "shorter then"(?) There is,
of course, no reason to expect that geometries of H-bonds for parm96 + tip3p
would match those of parm96+ tip5p, or cvff + tip5p.
Hydrogen bond geometries between peptides and water are very bad with
parm94/96.dat + tip3p water. This was just one of the compromises that
was made when the force field was developed. Some discussion of this
point is in:
%A P. Cieplak
%A J. Caldwell
%A P. Kollman
%T Molecular Mechanical Models for Organic and Biological Systems Going Beyond
%the Atom Centered Two Body Additive Approximation: Aqueous Solution Free
%Energies of Methanol and N-Methyl Acetamide, Nucleic Acid Base, and Amide
%Hydrogen Bonding and Chloroform/Water Partition Coefficients of the Nucleic
%Acid Bases
%J J. Computat. Chem.
%V 22
%P 1048-1057
%D 2001
(see esp. Table V of this paper.) But I have no experience with tip5p
myself.
...good luck...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Thu Mar 13 2003 - 20:53:02 PST
