From owner-chemistry@ccl.net Sun Oct 4 12:13:01 2009 From: "FyD fyd**q4md-forcefieldtools.org" To: CCL Subject: CCL:G: R.E.D.-III.3 tools release - q4md-forcefieldtools.org Message-Id: <-40407-091004113859-12811-3NFRUlseiyP5otACz449wQ .. server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sun, 04 Oct 2009 16:37:06 +0200 MIME-Version: 1.0 Sent to CCL by: FyD [fyd^^^q4md-forcefieldtools.org] Dear All, I am pleased to announce the release of the program RESP ESP charge =20 Derive version III.3 (or R.E.D. III.3) and its related tools =20 (Ante_R.E.D.-1.3 and X R.E.D. III.3) available - - =20 http://q4md-forcefieldtools.org/RED/. New features available: - Bug corrections in R.E.D. III.2, - Portability on Windows platforms through the Cygwin environment =20 making the R.E.D. tools fully functional on UNIX, MacIntosh and =20 Windows operating systems (thanks to the contribution of T. Patko - =20 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 =20 WinGAMESS, - Implementation of a new Re_Fit mode allowing charge re-fitting and =20 force field library re-building from a previous R.E.D. run, - Development of the Mini-Howto and creation of a History file =20 summarizing the features implemented in the R.E.D. tools, - Creation of a benchmark of charge values for models with an =20 automatic checking procedure & connection with R.E.DD.B. - New manuals (History, Howto and Guides) are available in the PDF =20 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 =20 need to register again: She/he can use her/his R.E.D.-III tools =20 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 =20 step in molecular dynamics simulations based on AMBER, CHARMM, GLYCAM =20 and OPLS force fields. To derive such atom-centered charges three =20 steps need to be followed: - First, the molecule studied is optimized to determine a stable =20 minimum (using a quantum chemistry software). - Then, this minimized structure is used to calculate a Molecular =20 Electrostatic Potential (MEP) on a three-dimensional grid (using again =20 a quantum chemistry software). - Finally, this grid is exported into the "RESP program" (also =20 downloadable from the CCL software database) which is used to fit =20 atom-centered charges to the MEP. Although this method is now used 'routinely' to obtain partial charges =20 for molecules, in our opinion, it suffers from a number of limitations: - To apply this strategy, which requires the described above steps but =20 also numerous format conversions between the different programs used, =20 a significant number of scripts, programs and compilers are needed and =20 used sequentially. Consequently, the procedure is tedious, =20 time-consuming, and numerous errors can be introduced without having a =20 real way to check them. - Although it is admitted that any quantum chemistry programs could be =20 used to minimize the starting structure and to calculate the MEP, the =20 "Amber" developers mainly use the "Gaussian" program, which is a quite =20 expensive proprietary software. The "GAMESS" academic program, which =20 is provided at no cost and which provide similar functionality for =20 'RESP' and 'ESP' charges development than "Gaussian", is not =20 officially used to derive 'RESP' or 'ESP' charges. Indeed, it is known =20 that partial charges calculated using "GAMESS", are 'different' than =20 those determined using "Gaussian". - Finally, starting from different sets of Cartesian coordinates for a =20 same molecule, the 'RESP' or 'ESP' partial charges are, in somes =20 cases, not reproducible even using "Gaussian", making errors in the =20 protocol difficult to detect. Thus, we developed the R.E.D. I (RESP ESP charge Derive, version 1.0) =20 program to automatically derive 'RESP' and 'ESP' charges starting from =20 an un-optimized PDB structure. R.E.D. sequentially executes (i) either =20 the "GAMESS" program or the "Gaussian" program to minimize the target =20 structure and to compute the corresponding MEP, and (ii) the "RESP" =20 program to fit the atom-centered charges to the grid previously =20 determined. Format conversions needed during the procedure and =20 "GAMESS", "Gaussian" and "RESP" inputs are automatically generated by =20 R.E.D. By controlling the molecular orientation of the optimized =20 geometry, a new RESP fitting procedure based on multi-orientation =20 feature is proposed and results in highly reproducible 'RESP' and =20 'ESP' charges independently of the QM software or the initial =20 Cartesian coordinate set. With R.E.D. II (version 2.0), multi-conformation RESP and ESP fit has =20 been implemented. Such an approach permits to make the atom charge =20 values more 'general' and effective, and is useful in molecular =20 dynamics simulations where the whole conformational space needs to be =20 explored. Thus with R.E.D.-II, 'multi-conformation' and =20 'multi-orientation' RESP fit can be performed together or =20 independently according to the user choice. 'Standard' but also =20 'non-standard' RESP inputs can also be generated. Finally, RESP and =20 ESP charges can be derived for chemical elements having up to a total =20 number of electrons, Z =3D 35. With R.E.D. III.x (version 3.x), the control of charge constraints for =20 atoms and groups of atoms in a molecule (intra-molecule charge =20 constraint) or between two molecules (inter-molecule charge constraint =20 and inter-molecular charge equivalencing) has been incorporated =20 allowing for the derivation of the RESP and ESP atom charge values for =20 molecule fragments and sets of molecules. Fitting procedures involving =20 multiple molecules, and for each molecule, multiple conformations, and =20 for each conformation, multiple orientations, can now be automatically =20 carried out. Moverover, eight different charge derivation procedures =20 using different MEP computation algorithms (Connolly surface and =20 CHELPG algorithms) and different fitting procedures (with or without =20 hyperbolic restraints) are now available. Potentially, an infinite =20 number of approaches can be developed by simply changing a few words =20 in the R.E.D. III.x source code. Such procedures can be used in =20 simulations based on AMBER, CHARMM, GLYCAM and OPLS force fields. Once the R.E.D. execution is completed, the charge values are =20 available in Tripos mol2 file(s) which can be considered as precursors =20 of AMBER OFF and CHARMM RFT or PSF force field libraries. R.E.D. makes =20 the development of the 'RESP' and 'ESP' charges a straightforward, =20 simple and highly reliable procedure. R.E.D. interfaces the GAMESS-US or Gaussian program and RESP program. =20 R.E.D. III.x is now fully compatible with GAMESS-US (and its WinGAMESS =20 version), PC-GAMESS/Firefly and the Gaussian 1994, 1998, 2003 and 2009 =20 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 =20 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 =20 particular the "P2N" files. The P2N file format is a new file format =20 introduced with R.E.D. III. It corresponds to the PDB file format with =20 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 =20 R.E.D. III.x tools. R.E.D. (versions 1, 2 and 3.x) and Ante_R.E.D. have been written with =20 the "Perl" programming language, while X R.E.D. has been developed =20 using the "tcl/tk" programming language. "Perl" and "tcl/tk" are =20 interpreted programming languages, meaning that the programs written =20 with these languages do not need to be compiled. This makes R.E.D., =20 Ante_R.E.D. and X R.E.D. simple to use, highly flexible and portable. =20 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 =20 "freedom"; see the GNU web site for a clear definition). They are =20 provided at no cost for ACADEMIC users involved in NON-PROFIT RESEARCH =20 after signing a license. Industrial/COMMERCIAL users are asked to pay =20 3000.00 ? for using the R.E.D.III.x tools. The PI (Principal =20 Investigator or Director) of a laboratory has to be registered as a =20 R.E.D. III or R.E.D. III.x user to be authorized to download the =20 R.E.D. III.x tools (indeed, we do not accept anymore user agreement =20 > from students or post-doc). During the registration procedure, the PI =20 has to select a license among the four different licenses available: (1) License for Academic user & Non-profit research - User from north =20 & south America, (2) License for Academic user & Non-profit research - User from Europe =20 & the rest of the world, (3) License for Profit research (academic & non-academic user) - User =20 > from north & south America, (4) License for Profit research (academic & non-academic user) - User =20 > from Europe & the rest of the world. Please, see the Register section from the R.E.D. home page to =20 register, and display these licenses. If you have questions about the R.E.D. III.x tools, please, first =20 check the documentation available (i. e. the manuals and FAQ). Basic =20 tutorials are available in the R.E.D. I and R.E.D. II manuals, and new =20 Tutorials have been written to describe Ante_R.E.D.-1.x, R.E.D. III.x =20 and also R.E.DD.B.. If you need help about using the R.E.D. III.x tools, a general public =20 help is now provided with the q4md-forcefieldtools mailing list. Any =20 researcher can participate in this mailing list by answering and/or =20 sending queries at q4md-fft- -q4md-forcefieldtools.org after =20 registration at sympa- -q4md-forcefieldtools.org. To register in the =20 q4md-fft mailing list just send an email to =20 sympa- -q4md-forcefieldtools.org with "subscribe q4md-fft" in the email =20 subject or body (to un-subscribe just send "unsubscribe q4md-fft"). =20 Archives of the q4md-fft mailing list are public. We are also registered in the AMBER and CCL mailing lists, and we will =20 answer to the queries about the q4md force field tools in these two =20 mailing lists as well. If you have any suggestions about the R.E.D. III.x tools or if you =20 find a bug, send us an e-mail - - contact- -q4md-forcefieldtools.org regards, Francois F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/