AMBER Archive (2009)

Subject: [AMBER] R.E.D.-III.3 tools release - q4md-forcefieldtools.org

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sun Oct 04 2009 - 09:37:06 CDT

Dear All,

I am pleased to announce the release of the program RESP ESP charge
Derive version III.3 (or R.E.D. III.3) and its related tools
(Ante_R.E.D.-1.3 and X R.E.D. III.3) available @
http://q4md-forcefieldtools.org/RED/.

New features available:
- Bug corrections in R.E.D. III.2,
- Portability on Windows platforms through the Cygwin environment
making the R.E.D. tools fully functional on UNIX, MacIntosh and
Windows operating systems (thanks to the contribution of T. Patko -
California State University, Long Beach, CA, USA),
- Interface of Gaussian 2009 is implemented (as for g03, g98 & g94),
- Improvement of GAMESS-US & PC-GAMESS interface & new interface for
WinGAMESS,
- Implementation of a new Re_Fit mode allowing charge re-fitting and
force field library re-building from a previous R.E.D. run,
- Development of the Mini-Howto and creation of a History file
summarizing the features implemented in the R.E.D. tools,
- Creation of a benchmark of charge values for models with an
automatic checking procedure & connection with R.E.DD.B.
- New manuals (History, Howto and Guides) are available in the PDF
file format. See the "Documentation" section from the R.E.D. web site

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.3 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 (and its WinGAMESS
version), PC-GAMESS/Firefly and the Gaussian 1994, 1998, 2003 and 2009
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.x, and X R.E.D. III.x 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, 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.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.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 @ contact_at_q4md-forcefieldtools.org

regards, Francois

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

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