AMBER Archive (2007)

Subject: AMBER: Release of the R.E.D.-III tools

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sun Apr 15 2007 - 05:10:25 CDT

April, 15th, 2007.

Dear All,

We are pleased to announce the release of the program RESP ESP charge
Derive version III (or R.E.D. III) and its related tools (Ante_R.E.D.
and X R.E.D. III) available @ http://q4md-forcefieldtools.org/RED/.

With the R.E.D. version I, highly reproducible RESP and ESP charge
values (+/- 0.0001 e) can be derived by controlling the molecular
orientation of the optimized geometry of a single conformation of a
single molecule whichever the QM program or initial structure choice
is. A new charge derivation procedure has been developed based on
multi-orientation RESP or ESP fit. The use of multiple molecular
orientations in the fitting process is supposed to limit the charge
uncertainty induced when using a single orientation.

With the R.E.D. version II, the use of multiple conformations of a
single molecule in the fitting procedure has been implemented allowing
for the derivation of charge values of high quality (i. e. more
general; needed in molecular dynamics simulation). Multi-conformation
and multi-orientation RESP or ESP fit can be performed together or
independently for structures containing chemical elements of the
periodic table up to Z = 35 (Bromine) according to the user's choice.

With the R.E.D. version III, the control of charge constraints for
atoms and groups of atoms in a molecule or a set of molecules
(intra-molecule charge constraint) or between two molecules
(inter-molecule charge constraint and inter-molecular charge
equivalencing) has been developed allowing for the derivation of the
RESP and ESP atom charge values for molecule fragments and sets of
molecules. Thus, fitting procedures involving multiple molecules, and
for each molecule, multiple conformations, and for each conformation,
multiple orientations, can now be automatically carried out. Finally,
eight different charge derivation procedures using different MEP
computation algorithms (Connolly surface and CHELPG algorithms) and
different fitting procedures (with or without hyperbolic restraints)
are now available. Potentially, an infinite number of approaches can
be developed by simply changing a few words in the R.E.D. III source
code. Such procedures can be used in simulations based on AMBER,
CHARMM, OPLS and GLYCAM force fields.

Once the R.E.D. execution has correctly completed, the charge values
are available in Tripos mol2 file(s) which can be considered as
precursors of AMBER OFF and CHARMM RFT or PSF force field libraries.
R.E.D. makes the development of the 'RESP' and 'ESP' charges a
straightforward, simple and highly reliable procedure.

R.E.D. is an interface to the GAMESS-US (available @
http://www.msg.ameslab.gov/GAMESS/) or Gaussian (available @
http://www.gaussian.com/) program and RESP program (available @
http://amber.scripps.edu/Questions/resp.html). R.E.D. III is now fully
compatible with GAMESS-US, PC-GAMESS
(http://classic.chem.msu.su/gran/gamess/) and Gaussian 1994, 1998 and
2003 versions.

R.E.D. III is distributed with two other programs:
- X R.E.D. is a graphical user-friendly interface, which has been
developed to graphically execute R.E.D. and modify R.E.D. variables.
- Ante_R.E.D. is a program useful for preparing R.E.D. III inputs, and
in particular the "P2N" files. The P2N file format is a new file
format introduced with R.E.D. III. It derives from the PDB file
format, and corresponds to the PDB file format to whom one has added a
second column of atom names.
R.E.D. III, Ante_R.E.D., and X R.E.D. III constitute the R.E.D. III tools.

R.E.D. (versions 1, 2 and 3) and Ante_R.E.D. have been written with
the "Perl" programming language (See also the O'REILLY web site),
while X R.E.D. has been developed using the "tcl/tk" programming
language. "Perl" and "tcl/tk" are interpreted programming languages,
meaning that the programs written with these languages do not need to
be compiled. This makes R.E.D., Ante_R.E.D. and X R.E.D. simple to
use, highly flexible and portable. They have been tested on PC-LINUX
and SGI-IRIX workstations, and should work on all other UNIX platforms.

The R.E.D. III tools are not "FREE" programs (i. e. in the sense of
"freedom"; see the GNU web site
http://www.gnu.org/philosophy/philosophy.html for a clear definition).
They are provided at no cost for ACADEMIC users involved in NON-PROFIT
RESEARCH after signing a license. A 3000.00 Euros fee is demanded to
INDUSTRIAL/COMMERCIAL users and to ACADEMIC users involved in
PROFIT-RESEARCH for the use of the R.E.D. III tools. The PI (Principal
Investigator or Director) of a laboratory has to be registered as a
R.E.D. III user to be authorized to download the R.E.D. III tools.
During the registration procedure, the laboratory PI has to select a
license among the four different licenses available:
(1) License for Academic user & Non-profit research - User from north
& south America,
(2) License for Academic user & Non-profit research - User from Europe
& the rest of the world,
(3) License for Profit research (academic & non-academic user) - User
from north & south America,
(4) License for Profit research (academic & non-academic user) - User
from Europe & the rest of the world.
Please, see the Register section from the R.E.D. home page to
register, and display these licenses.

Two Tutorials available @ http://q4md-forcefieldtools.org/Tutorial/
have been written. The first one presents different RESP charge
derivation approaches using the Ante_R.E.D. and R.E.D. III programs.
The second one describes the R.E.DD.B. database. Many examples and
choices made are described, and whole data generated from R.E.D. III
runs are available for download.

Examples of RESP and ESP charge derivation performed using the R.E.D.
III program are available in the RESP ESP charge DDataBase:

* RESP atomic charges for 10 solvent molecules based on the Connolly
surface algorithm and the HF/6-31G* theory level: Project "W-46"
(available @ http://q4md-forcefieldtools.org/REDDB/up/W-46/).

* RESP atomic charges for 10 solvent molecules based on the CHELPG
algorithm and the HF/6-31G* theory level: Project "W-47" (available @
http://q4md-forcefieldtools.org/REDDB/up/W-47/).

* ESP atomic charges for 10 solvent molecules based on the Connolly
surface algorithm and the HF/6-31G* theory level: Project "W-48"
(available @ http://q4md-forcefieldtools.org/REDDB/up/W-48/).

* ESP atomic charges for 10 solvent molecules based on the CHELPG
algorithm and the HF/6-31G* theory level: Project "W-49" (available @
http://q4md-forcefieldtools.org/REDDB/up/W-49/).

* RESP atomic charges for the 4 DNA and RNA nucleosides based on the
Connolly surface algorithm and the HF/6-31G* theory level: Project
"W-69" (available @ http://q4md-forcefieldtools.org/REDDB/up/W-69/)
and project "W-74" (available @
http://q4md-forcefieldtools.org/REDDB/up/W-74/).

* RESP atomic charges for the 4 DNA and RNA nucleosides based on the
CHELPG algorithm and the HF/6-31G* theory level (following a strategy
similar to that applied in the GLYCAM 2004 force field): Project
"W-73" (available @ http://q4md-forcefieldtools.org/REDDB/up/W-73/)
and project "W-78" (available @
http://q4md-forcefieldtools.org/REDDB/up/W-78/).

* RESP atomic charges for the central, (+)NH3-terminal,
(-)OOC-terminal, NH2-terminal and HOOC-terminal fragments of the
dimethylalanine amino acid based on the Connolly surface algorithm and
the HF/6-31G* theory level: Project "F-3" (available @
http://q4md-forcefieldtools.org/REDDB/up/F-3/), project "F-7"
(available @ http://q4md-forcefieldtools.org/REDDB/up/F-7/), project
"F-11" (available @ http://q4md-forcefieldtools.org/REDDB/up/F-11/),
project "F-15" (available @
http://q4md-forcefieldtools.org/REDDB/up/F-15/) and project "F-19"
(available @ http://q4md-forcefieldtools.org/REDDB/up/F-19/),
respectively.

* RESP atomic charges based on the Connolly surface algorithm and the
HF/6-31G* theory level for the 16 components of a force field topology
database useful for modeling regular DNA: Project "F-45" (available @
http://q4md-forcefieldtools.org/REDDB/up/F-45/) with a LEaP script
(available @ http://q4md-forcefieldtools.org/REDDB/up/F-45/script1.ff)
to convert the library precursors (Tripos format) into OFF files.

* RESP atomic charges based on the CHELPG algorithm and the HF/6-31G*
theory level for the 16 components of a force field topology database
useful for modeling regular DNA (following a strategy similar to that
applied in the GLYCAM 2004 force field): Project "F-49" (available @
http://q4md-forcefieldtools.org/REDDB/up/F-49/)

* Same as project F-45, but the phosphate is located at the O3'
position instead of the O5' one: Project "F-50" (available @
http://q4md-forcefieldtools.org/REDDB/up/F-50/).

* RESP atomic charges based on the Connolly surface algorithm and the
HF/6-31G* theory level for the 16 components of a force field topology
database useful for modeling regular RNA: Project "F-51" (available @
http://q4md-forcefieldtools.org/REDDB/up/F-51/) with a LEaP script
(available @ http://q4md-forcefieldtools.org/REDDB/up/F-51/script1.ff)
to convert the library precursors (Tripos format) into OFF files (up
to Project "F-56" (available @
http://q4md-forcefieldtools.org/REDDB/up/F-56/ for other RNA force
field topology databases).

* Unusual nucleotide projects: Project "F-57" (available @
http://q4md-forcefieldtools.org/REDDB/up/F-57/, Project "F-58"
(available @ http://q4md-forcefieldtools.org/REDDB/up/F-58/ and
Project "F-51" (available @
http://q4md-forcefieldtools.org/REDDB/up/F-59/).

More projects are obviously available in R.E.DD.B.; see the download
section of R.E.DD.B.

regards, Francois

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

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