[gmx-users] Release of the R.E.D.-III tools

[FyD]

April, 17th, 2007.

Dear Gromacs community,

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/