From chemistry-request@server.ccl.net Sat Apr 27 00:25:48 2002 Received: from hsc.usf.edu ([131.247.67.157]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g3R4PmA19154 for ; Sat, 27 Apr 2002 00:25:48 -0400 Received: through eSafe SMTP Relay 1019577668; Sat Apr 27 00:22:51 2002 Received: from hsc.usf.edu (out.moffitt.usf.edu [131.247.182.200]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with ESMTP id AAA14485 for ; Sat, 27 Apr 2002 00:25:42 -0400 (EDT) Message-ID: <3CCA2848.3060000@hsc.usf.edu> Date: Sat, 27 Apr 2002 00:25:44 -0400 From: Hunter Hunts User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.2) Gecko/20010726 Netscape6/6.1 X-Accept-Language: en-us MIME-Version: 1.0 To: ccl Subject: Running autodock jobs in succesion Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello all, Can anyone tell me how to set up serveral docking jobs at one time and then allow the computer to exicute them one after another? I would like to be able to have the computer doing jobs all night so that time is not wasted. Im running linux with autodock 3. Any ideas at all would be greatly appreciated. thank you ! From chemistry-request@server.ccl.net Fri Apr 26 22:01:57 2002 Received: from smtp.unc.edu ([152.2.1.241]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3R21vA17082 for ; Fri, 26 Apr 2002 22:01:57 -0400 Received: from bock.chem.unc.edu.smtp.unc.edu (bock.chem.unc.edu [152.2.48.182]) by smtp.unc.edu (8.12.2/8.12.2) with ESMTP id g3R21MQ1027400; Fri, 26 Apr 2002 22:01:22 -0400 (EDT) Sender: jochen@bock.chem.unc.edu Newsgroups: gnu.emacs.sources Cc: molpro-user , CCL Subject: molpro.el User-Agent: XEmacs/Gnus X-Attribution: Jochen X-Face: -%Z4EZ6iY'4m:wiK:!v Organization: University of North Carolina Date: 26 Apr 2002 22:01:22 -0400 Message-ID: Lines: 29 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" --=-=-= I have updated molpro.el to provide font-locking and done some minor changes. Molpro is a quantum chemistry package, for more information see ,---- | http://www.tc.bham.ac.uk/molpro/ `---- molpro.el is a Emacs major mode that aids the preparation of input files, job submission, and examination of output files. This code is a modified version of the package available at ,---- | http://www.tc.bham.ac.uk/molpro/molpro.el `---- Currently the font-lock keyword-lists are a little sparse, and it only works for lowercase. I am working on that. With this posting I am looking for comments and patches:)) Maybe this file does also make it back on the molpro web-page. Greetings, Jochen -- University of North Carolina phone: +1-919-962-4403 Department of Chemistry phone: +1-919-962-1579 Venable Hall CB#3290 (Kenan C148) fax: +1-919-843-6041 Chapel Hill, NC 27599, USA GnuPG key: 44BCCD8E --=-=-= Content-Type: application/emacs-lisp Content-Disposition: attachment; filename=molpro.el Content-Transfer-Encoding: 8bit ;;; molpro-mode.el ;; Version 2.0pre1 ;; $Date: 2002/04/27 01:59:08 $ ;; $Revision: 1.5 $ ;; This is a major mode supporting the editing of molpro input files. ;; ;; It does font-locking, provides a menu to interactively run molpro, defines ;; some useful abbreviations, and also helps with the formatting. ;; Changes: ;; * April 2002, Jochen Küpper: ;; - Implemented font-locking. ;; - Bind '\t' to indent-relative-maybe ;; - Define more abbreviations. (require 'font-lock) (defvar molpro-mode-syntax-table nil "Syntax table used while in Molpro mode.") (defvar molpro-mode-abbrev-table nil "Abbrev table used while in Molpro mode.") (define-abbrev-table 'molpro-mode-abbrev-table ()) (define-abbrev molpro-mode-abbrev-table ";b" "basis" nil) (define-abbrev molpro-mode-abbrev-table ";d" "dummy" nil) (define-abbrev molpro-mode-abbrev-table ";fi" "file" nil) (define-abbrev molpro-mode-abbrev-table ";fr" "frequencies" nil) (define-abbrev molpro-mode-abbrev-table ";g" "geometry={}" nil) (define-abbrev molpro-mode-abbrev-table ";o" "opt" nil) (define-abbrev molpro-mode-abbrev-table ";s" "show," nil) (define-abbrev molpro-mode-abbrev-table ";t" "text," nil) (if molpro-mode-syntax-table () (setq molpro-mode-syntax-table (make-syntax-table)) (modify-syntax-entry ?\' "\"" molpro-mode-syntax-table) (modify-syntax-entry ?\! "<" molpro-mode-syntax-table) (modify-syntax-entry ?\n ">" molpro-mode-syntax-table)) (defvar molpro-mode-map nil "Keymap for Molpro mode.") (defvar molpro-mode-make-map nil "Keymap for Molpro-develop mode.") (if molpro-mode-map () (setq molpro-mode-map (make-sparse-keymap)) (if (string-match "XEmacs" emacs-version) (set-keymap-name molpro-mode-map 'molpro-mode-map)) (define-key molpro-mode-map ";" 'molpro-abbrev-start) (define-key molpro-mode-map "\t" 'indent-relative-maybe) (define-key molpro-mode-map "\C-c\C-c" 'molpro-run) (define-key molpro-mode-map "\C-c\C-b" 'molpro-run-background) (define-key molpro-mode-map "\C-c\C-q" 'molpro-run-batch) (define-key molpro-mode-map "\C-c\C-k" 'molpro-kill-for-buffer) (define-key molpro-mode-map "\C-c\C-l" 'molpro-show-output-buffer) (define-key molpro-mode-map "\C-c\C-r" 'molpro-mode-reload) ) (if molpro-mode-make-map () (setq molpro-mode-make-map (make-sparse-keymap)) (if (string-match "XEmacs" emacs-version) (set-keymap-name molpro-mode-make-map 'molpro-mode-make-map)) (define-key molpro-mode-make-map ";" 'molpro-abbrev-start) (define-key molpro-mode-make-map "\t" 'indent-relative-maybe) (define-key molpro-mode-make-map "\C-c\C-c" 'molpro-make-run) (define-key molpro-mode-make-map "\C-c\C-b" 'molpro-make-run-background) (define-key molpro-mode-make-map "\C-c\C-q" 'molpro-make-run-batch) (define-key molpro-mode-make-map "\C-c\C-k" 'molpro-kill-for-buffer) (define-key molpro-mode-make-map "\C-c\C-l" 'molpro-show-output-buffer) (define-key molpro-mode-make-map "\C-c\C-r" 'molpro-mode-reload) ) (defvar molpro-font-lock-keywords (let ((keyword (mapconcat 'identity '("\\*\\*\\*" "---" "active" "inactive" "angstrom" "degree" "average" "isotope" "do" "enddo" "if" "file" "mass" "molden" "noorient" "print" "put" "show" "text" ) "\\|")) ;; basis sets (basis (mapconcat 'identity '("cc-pVDZ" "cc-pVTZ" "cc-pVQZ" "aug-cc-pVDZ" "aug-cc-pVTZ" "aug-cc-pVQZ" ) "\\|")) ;; calculation methods (method (mapconcat 'identity '("HF" "RHF" "UHF" "MP2" "MP4" "CCSD" "RCCSD" "CCSD(T)" "RCCSD(T)" ) "\\|")) ;; functions (function (mapconcat 'identity '("add" "dummy" "energy" "frequencies" "forces" "opt" "optg" ) "\\|")) ;; variables (variable (mapconcat 'identity '("angles" "energy" "gradient" "basis" "geometry" "gprint" "gthresh" "optconv" "optstep" "optenergy" "optgrad" "spin" ) "\\|")) ) (list ;; basis sets (types) (cons (concat "=[ \t]*\\(" basis "\\)") '(1 font-lock-type-face)) ;; functions (functions) (cons (concat "\\(" function "\\)[ ,\n\t]") '(1 font-lock-function-name-face)) ;; methods (variables) (cons (concat "\\(" method "\\)[ \n\t]") '(1 font-lock-variable-name-face)) ;; variables (variables) (cons (concat "\\(" variable "\\)[=,\. \n\t]") '(1 font-lock-variable-name-face)) ;; keywords (keywords) (cons (concat "\\b\\(" keyword "\\)[,;\= \n\t([]") 1) ;; options (cons (concat "\\bshow\\(\\[.*\\]\\)") 1) '("\\([tT][eE][xX][tT],\\|\\*\\*\\*,\\) \\(.*\\)" 2 font-lock-comment-face t) ;; comments (yes, besides the default. We want to override everything else in them:) '("\\(!.*\\)" 1 font-lock-comment-face t) )) "Keywords and expressions to highlight in Molpro mode.") (put 'molpro-mode 'font-lock-defaults '((molpro-font-lock-keywords) t t)) (setq molpro-processname "Molpro") (defun molpro-mode-reload () (interactive) (defvar molpro-mode-map nil) (defvar molpro-mode-make-map nil) (defvar molpro-font-lock-keyword nil) (load-library "molpro") (molpro-mode) ) (defun molpro-check-saved () (setq require-final-line t) (save-buffer) ) (defun molpro-run-background () (interactive) (molpro-check-saved) (let ((procname (concat "*Running " (buffer-name)))) (if (molpro-kill procname) (message "Job aborted") (if (setq molpro-running (start-process procname procname "molpro" (buffer-name))) (progn (message "Molpro job started; use C-cC-l to see output") (set-process-sentinel molpro-running 'molpro-running-sentinel) ) (message "Error in spawning Molpro job"))))) ;;(setq molpro-nqs-queue "long") (defvar molpro-nqs-queue nil "NQS queue for Molpro jobs") (defun molpro-run-nqs () (interactive) (molpro-check-saved) (if molpro-nqs-queue () (setq molpro-nqs-queue (read-from-minibuffer "NQS queue: "))) (let ((proc (start-process "Nqs" "*Nqs log" "qsub" "-eo" "-q" molpro-nqs-queue "-r" (buffer-name)))) (if proc (progn (process-send-string proc (concat "cd " (default-directory) "\n")) (process-send-string proc (concat "molpro " (buffer-name) "\n")) (process-send-eof proc) ) (message "Error in submitting batch job")))) (defun molpro-run-batch () (interactive) (molpro-check-saved) (if molpro-batch-script () (setq molpro-batch-script (read-from-minibuffer "Batch command: "))) (let ((proc (start-process "Batch" "*Batch log" molpro-batch-script "-eo" "-q" molpro-nqs-queue "-r" (buffer-name)))) (if proc (progn (process-send-string proc (concat "cd " (default-directory) "\n")) (process-send-string proc (concat "molpro " (buffer-name) "\n")) (process-send-eof proc) ) (message "Error in submitting batch job")))) (defun molpro-run () "Run molpro" (interactive) (let ((molpro-output-buffer (concat "*Molpro output from " (buffer-name))) (molpro-input-buffer (buffer-name))) (if (molpro-kill) (message "Job aborted") (if (get-buffer molpro-output-buffer) (save-excursion (set-buffer molpro-output-buffer) (setq buffer-read-only nil) (erase-buffer) ) ) (setq proc (start-process molpro-processname molpro-output-buffer "molpro")) (set-buffer molpro-input-buffer) (setq molpro-running proc) (set-process-sentinel proc 'molpro-running-sentinel) (process-send-string proc (buffer-substring (point-min) (point-max))) (process-send-eof proc) (molpro-show-output-buffer) ) ) ) (defun molpro-running-sentinel (proc msg) ;; (princ ;; (format "Process: %s had the event %s" proc msg )) ;; (princ ;; (format "Process: %s has status %s and exit status %s" proc (process-status proc) (process-exit-status proc))) ;;(message (concat "sentinel: " "status:" (symbol-name (process-status proc)) ":" (process-exit-status proc))) (if (equal (symbol-name (process-status proc)) "exit") (progn (setq molpro-running nil) (if (equal (process-exit-status proc) 0) (message "Molpro run finished") (princ (format "Error in Molpro run, rc=%d\n" (process-exit-status proc))))) (message "Warning: unexpected entry to Molpro sentinel routine") ) ) (defun molpro-kill-for-buffer () "Kill any running Molpro process for the current buffer." (interactive) (molpro-kill) (molpro-kill (concat "*Running " (buffer-name))) ) (defun molpro-kill (&optional procname) "Kill current molpro process. Returns nil if process gone, t otherwise" (if procname () (setq procname molpro-processname)) (if (get-process procname) (progn (let ((killit (read-from-minibuffer "Do you want to kill active process? " ))) (if (equal (downcase (substring killit 0 1)) "y") (progn (delete-process procname) (message (concat "Killed process " procname))) t))) nil)) (defun molpro-output-file-name (input) (if (string-match "\\..*$" input) (replace-match ".out" t t input) (concat input ".out"))) (defun molpro-show-output-buffer () "Show Molpro output buffer" (interactive) ;;(delete-other-windows) (catch 'nooutput (progn ;; open the output file in view mode (setq molpro-output-buffer (concat "*Molpro output from " (buffer-name))) (let ((ob (get-buffer molpro-output-buffer)) (of (molpro-output-file-name (buffer-name)))) (cond ((buffer-live-p ob) (view-buffer ob)) ((file-exists-p of) (view-file of)) (t (progn (message "no output buffer or file") (throw 'nooutput nil)))) ) (if (string-match "XEmacs" emacs-version) (set-extent-property (make-extent (point-max) (point-min)) 'face 'molpro-output-face)) (setq truncate-lines t) (if viper-current-state (viper-change-state-to-emacs)) (setq mode-name "Molpro-output") )) ) (setq compile-command "make") (defun molpro-make () "Run make in the current directory" (interactive) (setq compilation-finish-function nil) (compile compile-command)) (defun molpro-make-run () "Run make in the current directory, and run Molpro on the current buffer if successful" (interactive) (molpro-make-and-run 'molpro-run) ) (defun molpro-make-run-background () "Run make in the current directory, and run Molpro on the current buffer's file if successful" (interactive) (molpro-make-and-run 'molpro-run-background) ) (defun molpro-make-run-batch () "Run make in the current directory, and batch submit Molpro on the current buffer's file if successful" (interactive) (molpro-make-and-run 'molpro-run-batch) ) (defun molpro-make-and-run (runner) (setq molpro-input (buffer-name)) (setq molpro-runner runner) (setq compilation-finish-function '(lambda (buf msg) (if (equal (substring msg 0 8) "finished") (progn (set-buffer molpro-input) (compilation-minor-mode 0) (delete-other-windows) (funcall molpro-runner))))) (compile compile-command)) (defun molpro-mode () "Major mode for editing Molpro input Special commands: \\{molpro-mode-map} Turning on Molpro mode calls the value of the variable `molpro-mode-hook', if that value is non-nil. Type ;? or ;\\[help-command] to display a list of built-in\ abbrevs for Molpro keywords. " (interactive) (kill-all-local-variables) (make-local-variable 'comment-start) (make-local-variable 'comment-end) (make-local-variable 'font-lock-defaults) (if (file-exists-p "base/develop/Makefile") (use-local-map molpro-mode-make-map) (use-local-map molpro-mode-map)) (setq comment-start "!" comment-end "" mode-name "Molpro" major-mode 'molpro-mode local-abbrev-table molpro-mode-abbrev-table font-lock-defaults '(molpro-font-lock-keywords)) (set-syntax-table molpro-mode-syntax-table) (defvar molpro-running nil "List of Molpro processes now running.") (or (assq 'molpro-running minor-mode-alist) (setq minor-mode-alist (cons '(molpro-running " Molpro-run") minor-mode-alist))) (make-face 'molpro-input-face) (copy-face 'default 'molpro-input-face) ;; (set-face-background 'molpro-input-face "limegreen") (make-face 'molpro-output-face) (copy-face 'molpro-input-face 'molpro-output-face) ;; (set-face-background 'molpro-output-face "pink") (if (string-match "XEmacs" emacs-version) (progn (make-face-smaller 'molpro-output-face) (set-extent-property (make-extent (point-max) (point-min)) 'face 'molpro-input-face) ;; menus (set-buffer-menubar (copy-sequence current-menubar)) (if (file-exists-p "base/develop/Makefile") (add-submenu nil molpro-xemacs-develop-menu) (add-submenu nil molpro-xemacs-menu)))) (run-hooks 'molpro-mode-hook)) ;; menus (if (string-match "XEmacs" emacs-version) (progn (defvar molpro-xemacs-menu '("Molpro" ["Run interactive" molpro-run t] ["Run background" molpro-run-background t] ["Run batch" molpro-run-batch t] ["Display output" molpro-show-output-buffer t] ["Kill" molpro-kill-for-buffer t] "-----" ["Reload mode" molpro-mode-reload t]) "XEmacs menu for Molpro mode.") (defvar molpro-xemacs-develop-menu '("Molpro" ["Run interactive" molpro-run t] ["Run background" molpro-run-background t] ["Run batch" molpro-run-batch t] ["Display output" molpro-show-output-buffer t] ["Kill" molpro-kill-for-buffer t] "-----" ["Make" molpro-make t] ["Make & run interactive" molpro-make-run t] ["Make & run background" molpro-make-run-background t] ["Make & run batch" molpro-make-run-batch t] "-----" ["Reload mode" molpro-mode-reload t]) "XEmacs menu for Molpro mode."))) (defun molpro-abbrev-start () "Typing ;\\[help-command] or ;? lists all the Fortran abbrevs. Any other key combination is executed normally." (interactive) ;; XEmacs change (let (e c) (insert last-command-char) (setq e (next-command-event) c (event-to-character e)) ;; insert char if not equal to `?' (if (or (= c ??) (eq c help-char)) (molpro-abbrev-help) (setq unread-command-events (list e))))) (defun molpro-abbrev-help () "List the currently defined abbrevs in Fortran mode." (interactive) (message "Listing abbrev table...") (display-buffer (molpro-prepare-abbrev-list-buffer)) (message "Listing abbrev table...done")) (defun molpro-prepare-abbrev-list-buffer () (save-excursion (set-buffer (get-buffer-create "*Abbrevs*")) (erase-buffer) (insert-abbrev-table-description 'molpro-mode-abbrev-table t) (goto-char (point-min)) (set-buffer-modified-p nil) (edit-abbrevs-mode)) (get-buffer-create "*Abbrevs*")) (provide 'molpro) ;;; molpro-mode.el ends here ;; Local Variables: ;; fill-column: 79 ;; End: --=-=-=-- From chemistry-request@server.ccl.net Sat Apr 27 00:46:48 2002 Received: from web14602.mail.yahoo.com ([216.136.224.82]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g3R4kmA19465 for ; Sat, 27 Apr 2002 00:46:48 -0400 Message-ID: <20020427044641.76053.qmail@web14602.mail.yahoo.com> Received: from [203.87.132.164] by web14602.mail.yahoo.com via HTTP; Sat, 27 Apr 2002 05:46:41 BST Date: Sat, 27 Apr 2002 05:46:41 +0100 (BST) From: =?iso-8859-1?q?amor=20san=20juan?= Subject: AutoDock3 testing in Red Hat 7 linux To: CHEMISTRY@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello CClers: AutoDock 3 compiled in Red hat 7 linux runs successfully. However, faulty compilation occurs based on the data below: ------------------------------------------------------ AUTODOCK 3.0.5 TESTING ------------- 3ptb + benzamidine ------------- [dostaas@sine 3ptb]$ ls -l total 11844 1 dostaas dostaas 2173 Mar 6 1999 3ptbA.gpf 1 dostaas dostaas 2472200 Mar 6 1999 3ptb.A.map 1 dostaas dostaas 2473088 Mar 6 1999 3ptb.C.map 1 dostaas dostaas 2129614 Oct 31 2000 3ptb.e.map 1 dostaas dostaas 2217491 Mar 6 1999 3ptb.H.map 1 dostaas dostaas 1298 Mar 6 1999 3ptb.maps.fld 1 dostaas dostaas 2429468 Mar 6 1999 3ptb.N.map 1 dostaas dostaas 155001 Mar 6 1999 3ptb.pdbq 1 dostaas dostaas 187263 Mar 6 1999 3ptb.pdbqs 1 dostaas dostaas 2338 Mar 6 1999 benA.3ptb.GA.dpf 1 dostaas dostaas 2761 Mar 6 1999 benA.3ptb.GASW.dpf 1 dostaas dostaas 2013 Mar 6 1999 benA.3ptb.SA.dpf 1 dostaas dostaas 1294 Mar 6 1999 benA.pdbq ------------------------------------------------------- --------- RUN 1 --------- [dostaas@sine AutoDock3]$ ls -l |more total 9420 1 dostaas dostaas 1787397 Apr 25 09:40 3ptb.A.map 1 dostaas dostaas 1788277 Apr 25 09:40 3ptb.C.map 1 dostaas dostaas 1448576 Apr 25 09:40 3ptb.e.map 1 dostaas dostaas 202867 Apr 25 09:40 3ptb.glg 1 dostaas dostaas 2545 Apr 25 09:36 3ptb.gpf 1 dostaas dostaas 1536450 Apr 25 09:40 3ptb.H.map 1 dostaas dostaas 1299 Apr 25 09:38 3ptb.maps.fld 1 dostaas dostaas 40 Apr 25 09:38 3ptb.maps.xyz 1 dostaas dostaas 1744623 Apr 25 09:40 3ptb.N.map 1 dostaas dostaas 155001 Mar 6 1999 3ptb.pdbq1 1 dostaas dostaas 187263 Apr 25 09:34 3ptb.pdbqs 1 dostaas dostaas 81417 Apr 25 09:44 benA.3ptb.dlg 1 dostaas dostaas 4195 Apr 25 09:36 benA.3ptb.dpf 1 dostaas dostaas 1294 Mar 6 1999 benA.pdbq ----------------------------------------------------- Any guidance or suggestions will be grateful. Amor UP-Diliman Philippines __________________________________________________ Do You Yahoo!? Yahoo! Health - your guide to health and wellness http://health.yahoo.com From chemistry-request@server.ccl.net Fri Apr 26 21:01:11 2002 Received: from traven.uol.com.br ([200.231.206.184]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3R11AA16263 for ; Fri, 26 Apr 2002 21:01:11 -0400 Received: from uol.com.br ([200.191.184.128]) by traven.uol.com.br (8.9.1/8.9.1) with ESMTP id VAA26367 for ; Fri, 26 Apr 2002 21:50:07 -0300 (BRT) Message-ID: <3CC9F945.80709@uol.com.br> Date: Fri, 26 Apr 2002 22:05:09 -0300 From: Alexander Martins User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry Subject: Re: CCL:Locating a transition state References: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Hi, First of all, it's a good idea use DFT methods instead of semiempirical ones. The results ara more reliable. You can use the keyword OPT=(TS, NoEigenTest) with a good guess for the geometry. Futhermore, the keyword OPT=QST3 it's a good option too. Don't forget use a good basis set, like 6-31G. Try these sugestions. Good luck, Alexander. > > Hi, > > I am trying to locate a transition state for a system about 30 atoms > using an empirical > method. So far I haven't had any success. I would appreciate if you could > give me any suggestions. > > I am interested in a hydrolysis reaction pathway, using PM3 in > Gaussian 98: > > R-C-O-C-R' + H*-O'H ---> R-C-O-H* + H-O'-C-R' > > I have done the following: > 1) opt=Ts ; This always failed due to incorrect number of negative > frequencies. > 2) Scan ; I have not tried much. > 3) opt=ModRedundant: Scanning succeeded, but the population analysis after > the scanning seemed failed. The output did not indicate why it failed, but > the heading of population analysis appeared, followed by signal 11 error. > 4) opt=qst2; There is (are) one or two statement(s) "stationary point was > found" (the distances were the same for all, but the angles and > torsions were slightly different in the two stationary points) in the > output, but the optimization (?) kept going and failed; Optimization > aborted > --- No acceptable step or Inconsistency: ModMin= 2. > > I optimized two reactant molecules individually and moved them close > to make > a reaction. The products were also optimized. The order of the atoms are > exactly the same. > > > Thanks, > > Genzo Tanaka > Network Computing Services, Inc./ > Army High Performance Computing Research Center at FAMU > -- *************************************************************************** Alexander Martins da Silva emails: alex.msilva@uol.com.br Doutorando em Físico-Química alex@chaer.iq.ufrj.br Dept. de Físico-Química Phone: +55-21-2562-7179 (office) Universidade do Brasil, RJ, Brazil +55-21-2696-2676 (residence) *************************************************************************** From chemistry-request@server.ccl.net Sat Apr 27 12:23:23 2002 Received: from hotmail.com ([64.4.37.170]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3RGNNA24551 for ; Sat, 27 Apr 2002 12:23:23 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sat, 27 Apr 2002 09:23:12 -0700 Received: from 171.64.127.133 by pv2fd.pav2.hotmail.msn.com with HTTP; Sat, 27 Apr 2002 16:23:12 GMT X-Originating-IP: [171.64.127.133] From: "Bin Shan" To: Genzo.Tanaka@netaspx.com, chemistry@ccl.net Subject: Re: CCL:Locating a transition state Date: Sat, 27 Apr 2002 16:23:12 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 27 Apr 2002 16:23:12.0357 (UTC) FILETIME=[D37ED150:01C1EE07] Hi, Genzo,try something like this # opt(modredundant,TS,noeigen,CalcFC) rb3lyp/6-31g(d) nosymm CalcFC calculates the initial force constants be computed at the first point and helps to determine which direction the atoms are to to move.The keyword noeigen and nosymm are also important. And it is also extremely important to specify a good initial guess.Finding transition state is by no means an easy task...according to my experience. Good luck. Bin >From: Genzo.Tanaka@netaspx.com >To: chemistry@ccl.net >Subject: CCL:Locating a transition state >Date: Fri, 26 Apr 2002 15:51:46 -0400 > >Hi, > >I am trying to locate a transition state for a system about 30 atoms using >an empirical >method. So far I haven't had any success. I would appreciate if you could >give me any suggestions. > >I am interested in a hydrolysis reaction pathway, using PM3 in Gaussian >98: > >R-C-O-C-R' + H*-O'H ---> R-C-O-H* + H-O'-C-R' > >I have done the following: >1) opt=Ts ; This always failed due to incorrect number of negative >frequencies. >2) Scan ; I have not tried much. >3) opt=ModRedundant: Scanning succeeded, but the population analysis after >the scanning seemed failed. The output did not indicate why it failed, but >the heading of population analysis appeared, followed by signal 11 error. >4) opt=qst2; There is (are) one or two statement(s) "stationary point was >found" (the distances were the same for all, but the angles and torsions >were slightly different in the two stationary points) in the output, but >the optimization (?) kept going and failed; Optimization aborted >--- No acceptable step or Inconsistency: ModMin= 2. > >I optimized two reactant molecules individually and moved them close to >make >a reaction. The products were also optimized. The order of the atoms are >exactly the same. > > >Thanks, > >Genzo Tanaka >Network Computing Services, Inc./ >Army High Performance Computing Research Center at FAMU _________________________________________________________________ Chat with friends online, try MSN Messenger: http://messenger.msn.com From chemistry-request@server.ccl.net Sat Apr 27 15:06:13 2002 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3RJ65A25915 for ; Sat, 27 Apr 2002 15:06:13 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.6/TSRI-4.2rx) with SMTP id g3RJ5xw17905 for ; Sat, 27 Apr 2002 12:05:59 -0700 (PDT) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id 7792; Sat, 27 Apr 2002 12:03:56 -0700 (PDT) Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay1.scripps.edu (8.11.6/TSRI-4.2.1rAV) with ESMTP id g3RJ5m712565; Sat, 27 Apr 2002 12:05:48 -0700 (PDT) Received: from localhost (yadavm@localhost) by elvis.scripps.edu (8.9.2/TSRI-3.0.1) with SMTP id MAA338712; Sat, 27 Apr 2002 12:05:48 -0700 (PDT) Date: Sat, 27 Apr 2002 12:05:48 -0700 (PDT) From: Maneesh Yadav X-Sender: yadavm@elvis To: Hunter Hunts cc: ccl Subject: Re: CCL:Running autodock jobs in succesion In-Reply-To: <3CCA2848.3060000@hsc.usf.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII You can just do it on the command line with your shell probably autodock job1; autodock job2 etc... or make a script file that looks like #!/bin/csh autodock job1 autodock job2 etc. you may want to prefix with "nohup" if you want to be sure it'll run if even if you logout. From chemistry-request@server.ccl.net Sat Apr 27 19:10:48 2002 Received: from hsc.usf.edu ([131.247.67.157]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g3RNAmA27423 for ; Sat, 27 Apr 2002 19:10:48 -0400 Received: through eSafe SMTP Relay 1019577668; Sat Apr 27 19:07:47 2002 Received: from hsc.usf.edu (out.moffitt.usf.edu [131.247.182.200]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with ESMTP id TAA13516 for ; Sat, 27 Apr 2002 19:10:29 -0400 (EDT) Message-ID: <3CCB2FE6.6020209@hsc.usf.edu> Date: Sat, 27 Apr 2002 19:10:30 -0400 From: Hunter Hunts User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.2) Gecko/20010726 Netscape6/6.1 X-Accept-Language: en-us MIME-Version: 1.0 To: ccl Subject: EP and HP surface maps with pymol Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hellow again CCler's, Does any know how to color a surface map in Pymol with Electrostatic potensial and Hydrphobicity? Thanks for your suggestion.