[gmx-users] Release of the R.E.D.-III.4 tools

[FyD]

Dear All,

I am pleased to announce the release of the program RESP ESP charge  
Derive version III.4 (or R.E.D. III.4) and its related tools  
(Ante_R.E.D.-1.4 and X R.E.D. III.4) available @  
http://q4md-forcefieldtools.org/RED/.

New features available:
- Bug corrections and code cleaning in R.E.D. III.3,
- Development of the Mini-Howto,
- Tutorials have been updated,
- Charge reproducibility has been further developed: the rigid-body  
reorientation algorithm has been re-written allowing all users to  
differentiate translation, rotation from the original reorientation  
approach,
- Cartesian coordinates of molecular fragments originating from  
molecular fusion between two molecules are now recalculated allowing  
to generate correct geometries.

The R.E.D. III.4 tools are now distributed under the GNU General  
Public License after a simple Register & Download procedure.

The article describing the R.E.D. Tools is now available @  
http://www.rsc.org/publishing/journals/CP/article.asp?doi=c0cp00111b

News about the latest developments of R.E.D. IV can be found @  
http://q4md-forcefieldtools.org/RED/popup/news.php.


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 or from  
q4md-forcefieldtools) 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  
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 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 (and its WinGAMESS  
version), Firefly and the Gaussian 1994, 1998, 2003 and 2009 versions  
on UNIX, MacIntosh and Windows plateforms.

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.x, and X R.E.D. III.x constitute the  
R.E.D. III.x tools.

R.E.D. (versions I, II and III.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 are fully functional on UNIX,  
MacIntosh and Windows plateforms.

The R.E.D. III.4 tools are now distributed under the GNU General  
Public License after a simple Register & Download procedure.

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.x, 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 at contact at q4md-forcefieldtools.org.

regards, Francois


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