[gmx-users] Release of the R.E.D.-III.1 tools

[FyD]

Dear All,                                January, 12th, 2009.

I am pleased to announce the release of the program RESP ESP charge  
Derive version III.1 (or R.E.D. III.1) and its related tools  
(Ante_R.E.D.-1.1 & X R.E.D. III.1) available @  
http://q4md-forcefieldtools.org/RED/.

New features available:
- Bug corrections in Ante_R.E.D. & R.E.D.-III,
- Better handling/display of system variables,
- Better interface for PC-GAMESS/Firefly & GAMESS-US (Ante_R.E.D.,  
R.E.D. & X_R.E.D.),
- Portability on Mac OS X platforms (Thanks to T. Patko's work -  
California State University, Long Beach, CA, USA),
- Better compatibility with R.E.D. Server.

This new distribution contains a mini-HowTo and a tutorial about  
charge derivation and force field library building for whole molecules  
and molecule fragments using the R.E.D.-III.1 tools.

A person who is already registered as a R.E.D.-III tools user does not  
need to register again: She/he can use her/his R.E.D.-III tools  
login/passwd obtained previously to download the R.E.D.-III.1 tools.



         RESP and ESP charge derivation for a new structure is an  
important step in molecular dynamics simulations based on AMBER,  
CHARMM, GLYCAM and OPLS force fields. To derive such atom-centered  
charges three steps need to be followed:
- First, the molecule studied is optimized to determine a stable  
minimum (using a quantum chemistry software).
- Then, this minimized structure is used to calculate a Molecular  
Electrostatic Potential (MEP) on a three-dimensional grid (using again  
a quantum chemistry software).
- Finally, this grid is exported into the "RESP program" (also  
downloadable from the CCL software database) which is used to fit  
atom-centered charges to the MEP.

         Although this method is now used 'routinely' to obtain  
partial charges for molecules, in our opinion, it suffers from a  
number of limitations:
- To apply this strategy, which requires the described above steps but  
also numerous format conversions between the different programs used,  
a significant number of scripts, programs and compilers are needed and  
used sequentially. Consequently, the procedure is tedious,  
time-consuming, and numerous errors can be introduced without having a  
real way to check them.
- Although it is admitted that any quantum chemistry programs could be  
used to minimize the starting structure and to calculate the MEP, the  
"Amber" developers mainly use the "Gaussian" program, which is a quite  
expensive proprietary software. The "GAMESS" academic program, which  
is provided at no cost and which provide similar functionality for  
'RESP' and 'ESP' charges development than "Gaussian", is not  
officially used to derive 'RESP' or 'ESP' charges. Indeed, it is known  
that partial charges calculated using "GAMESS", are 'different' than  
those determined using "Gaussian".
- Finally, starting from different sets of Cartesian coordinates for a  
same molecule, the 'RESP' or 'ESP' partial charges are, in somes  
cases, not reproducible even using "Gaussian", making errors in the  
protocol difficult to detect.


         Thus, we developed the R.E.D. I (RESP ESP charge Derive,  
version 1.0) program to automatically derive 'RESP' and 'ESP' charges  
starting from an un-optimized PDB structure. R.E.D. sequentially  
executes (i) either the "GAMESS" program or the "Gaussian" program to  
minimize the target structure and to compute the corresponding MEP,  
and (ii) the "RESP" program to fit the atom-centered charges to the  
grid previously determined. Format conversions needed during the  
procedure and "GAMESS", "Gaussian" and "RESP" inputs are automatically  
generated by R.E.D. By controlling the molecular orientation of the  
optimized geometry, a new RESP fitting procedure based on  
multi-orientation feature is proposed and results in highly  
reproducible 'RESP' and 'ESP' charges independently of the QM software  
or the initial Cartesian coordinate set.

         With R.E.D. II (version 2.0), multi-conformation RESP and ESP  
fit has been implemented. Such an approach permits to make the atom  
charge values more 'general' and effective, and is useful in molecular  
dynamics simulations where the whole conformational space needs to be  
explored. Thus with R.E.D.-II, 'multi-conformation' and  
'multi-orientation' RESP fit can be performed together or  
independently according to the user choice. 'Standard' but also  
'non-standard' RESP inputs can also be generated. Finally, RESP and  
ESP charges can be derived for chemical elements having up to a total  
number of electrons, Z = 35.

         With R.E.D. III.x (version 3.x), the control of charge  
constraints for atoms and groups of atoms in a molecule  
(intra-molecule charge constraint) or between two molecules  
(inter-molecule charge constraint and inter-molecular charge  
equivalencing) has been incorporated allowing for the derivation of  
the RESP and ESP atom charge values for molecule fragments and sets of  
molecules. Fitting procedures involving multiple molecules, and for  
each molecule, multiple conformations, and for each conformation,  
multiple orientations, can now be automatically carried out.  
Moverover, 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.x source code. Such procedures can be used in  
simulations based on AMBER, CHARMM, GLYCAM and OPLS force fields.

         Once the R.E.D. execution is 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. interfaces the GAMESS-US or Gaussian program and RESP  
program. R.E.D. III.x is now fully compatible with GAMESS-US,  
PC-GAMESS/Firefly and Gaussian 1994, 1998 and 2003 versions.


         R.E.D. III.x 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.  
inputs, and in particular the "P2N" files. The P2N file format is a  
new file format introduced with R.E.D. III. It corresponds to the PDB  
file format with a second column of atom names.
         R.E.D. III.x, Ante_R.E.D.-1.1, and X R.E.D. III.1 constitute  
the R.E.D. III.x tools.

         R.E.D. (versions 1, 2 and 3.x) 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.x tools are not "FREE" programs (i. e. in the  
sense of "freedom"; see the GNU web site for a clear definition). They  
are provided at no cost for ACADEMIC users involved in NON-PROFIT  
RESEARCH after signing a license. Industrial/COMMERCIAL users are  
asked to pay 3000.00 ? for using the R.E.D.III.x tools. The PI  
(Principal Investigator or Director) of a laboratory has to be  
registered as a R.E.D. III or R.E.D. III.x user to be authorized to  
download the R.E.D. III.x tools (indeed, we do not accept anymore user  
agreement from students or post-doc). During the registration  
procedure, the 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.


         If you have questions about the R.E.D. III.x tools, please,  
first check the documentation available (i. e. the manuals and FAQ).  
Basic tutorials are available in the R.E.D. I and R.E.D. II manuals,  
and new Tutorials have been written to describe Ante_R.E.D.-1.1,  
R.E.D. III.x and also R.E.DD.B..

         If you need help about using the R.E.D. III.x tools, a  
general public help is now provided with the q4md-forcefieldtools  
mailing list. Any researcher can participate in this mailing list by  
answering and/or sending queries at q4md-fft at q4md-forcefieldtools.org  
after registration at sympa at q4md-forcefieldtools.org. To register in  
the q4md-fft mailing list just send an email to  
sympa at q4md-forcefieldtools.org with "subscribe q4md-fft" in the email  
subject or body (to un-subscribe just send "unsubscribe q4md-fft").  
Archives of the q4md-fft mailing list are public.

         We are also registered in the AMBER and CCL mailing lists,  
and we will answer to the queries about the q4md force field tools in  
these two mailing lists as well.

         If you have any suggestions about the R.E.D. III.x tools or  
if you find a bug, send us an e-mail: contact at q4md-forcefieldtools.org

regards, Francois

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