Release of the R.E.D.-III.5 tools

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Feb 22 2012 - 05:00:23 CST

Dear All,

  We are pleased to announce the release of the program RESP ESP
charge Derive version III.5 (or R.E.D. III.5) and its related tools
(Ante_R.E.D.-1.5 and X R.E.D. III.5) available @
http://q4md-forcefieldtools.org/RED/.

  New features available:
  - Bug corrections and code cleaning,
  - Update of the Mini-HowTo & Tutorials,
  - Better handling of Gaussian, GAMESS and Firefly error messages,
  - Charge value rounding off errors automatically corrected at 10-6
up to 10-2 depending on the user choice,
  - Handling geometrical constraints in the P2N file format (geometry
optimization using the Gaussian program),
  - Two new scripts for data submission in R.E.DD.B.,
  - New version for the RESP program: version 2.2 with updated documentation.

  The R.E.D. III.5 tools are distributed under the GNU General Public
License after a simple Register & Download procedure.

  The article describing the R.E.D. tools is available @
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/.

  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.5 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/

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