From chemistry-request@ccl.net Mon Jan 10 20:02:39 2005 Received: from sandmail01.sd.accelrys.com (rrcs-67-52-158-62.west.biz.rr.com [67.52.158.62]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0B12c69019009 for ; Mon, 10 Jan 2005 20:02:38 -0500 Importance: Normal X-Priority: 3 (Normal) Expiry-Date: Thu, 31 Mar 2005 -1:-1:-1 +0000 Reply-To: workshops..at..accelrys.com To: CHEMISTRY..at..ccl.net Subject: CCL: Accelrys Customer Training for March MIME-Version: 1.0 Sensitivity: X-Mailer: Lotus Notes Release 6.5.1 January 21, 2004 From: Jeff Nauss Message-ID: Date: Mon, 10 Jan 2005 17:19:52 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.5.2|June 01, 2004) at 01/10/2005 05:19:53 PM, Serialize complete at 01/10/2005 05:19:53 PM Content-Type: text/plain; charset="US-ASCII" X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Accelrys Inc. are holding the following training workshops at during March. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $520 per day for government and $380 per day for academic. BIOINFORMATICS Wisconsin Package and SeqLab 8-9 March Cambridge, UK SeqWeb 10 March Cambridge, UK DS Gene 11 March Cambridge, UK For course details and registration see: http://www.accelrys.com/training/bioinf/schedule.html MODELING Intro to DS Modeling 1.1 2-3 March San Diego, CA Structure Based Design with DS Modeling 1.2 4 March San Diego, CA For course details and registration see: http://www.accelrys.com/training/macro/schedule.html and http://www.accelrys.com/training/rdd/schedule.html CHEMINFORMATICS Accord Enterprise Clients 14 March San Diego, CA Accord Enterprise DBA 15-16 March San Diego,CA Accord HTS 17 March San Diego, CA Accord Inventory 18 March San Diego, CA For course details and registration see: http://www.accelrys.com/training/cheminf/schedule.html Questions regarding scheduling and content should be directed to workshops..at..accelrys.com -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training From chemistry-request@ccl.net Mon Jan 10 20:32:23 2005 Received: from mailhub2.uq.edu.au (mailhub2.uq.edu.au [130.102.149.128]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0B1WJ69021257 for >ccl.net>; Mon, 10 Jan 2005 20:32:20 -0500 Received: from smtp2.uq.edu.au (smtp2.uq.edu.au [130.102.5.53]) by mailhub2.uq.edu.au (8.12.11/8.12.11) with ESMTP id j0B1nbk0082488 for >ccl.net>; Tue, 11 Jan 2005 11:49:37 +1000 (EST) Received: from uq.edu.au (gonzo.soe.uq.edu.au [130.102.5.131]) by smtp2.uq.edu.au (8.12.10/8.12.10) with ESMTP id j0B1nbJh029705 for >ccl.net>; Tue, 11 Jan 2005 11:49:37 +1000 (EST) Received: from [152.98.207.35] by msg2b.soe.uq.edu.au (mshttpd); Tue, 11 Jan 2005 11:49:37 +1000 From: Dr Seth OLSEN >uq.edu.au> To: chemistry<>ccl.net Message-ID: >uq.edu.au> Date: Tue, 11 Jan 2005 11:49:37 +1000 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.21 (built Sep 8 2003) MIME-Version: 1.0 Content-Language: en Subject: CCL:GAMESS/TINKER - PROBLEM WITH DLC COORDINATES X-Accept-Language: en Priority: normal Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.43 on UQ Mailhub X-Spam-Status: No, hits=6.2 required=7.5 tests=IMPRONONCABLE_1, LINES_OF_YELLING,LINES_OF_YELLING_2,SUBJ_ALL_CAPS,TRACKER_ID autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Colleagues, My input for GAMESS/TINKER is a 98 atom peptide containing a modified tripeptide. The modified sequence is to be included in the QM/MM region of a GAMESS/TINKER optimization. I have included NZVAR=288 in the $CNTRL and my $ZMAT deck includes the directives DLC=.T. and AUTO=.T. However, the job fails with the error: ERROR: CURRENT QMMM IMPLEMENTATION REQUIRES DLC COORDINATES (SEE $ZMAT) The molecule does not contain any I have been reading the manual and experimenting with the input, as I anticipate that somehow I have failed to enter the combination of NZVAR and the $ZMAT deck in the correct manner. If one of you has time (or the error is sufficiently transparent to you), could you lend a hint? (Thanks to Brian Salter-Duke for his earlier help) My input deck follows: --$CNTRL EXETYP=CHECK $END $CNTRL SCFTYP=RHF RUNTYP=optimize MULT=1 EXETYP=RUN COORD=TINKER ICHARG=-1 NZVAR=288 $END $BASIS GBASIS=sto NGAUSS=3 $END $ZMAT DLC=.T. AUTO=.T. $END $TINXYZ 98 molden generated tinker .xyz (mm3 param.) 1 C 1.124320 -1.779122 -5.825405 20009 2 6 74 2 C 1.390048 -0.427314 -6.208361 20002 1 3 7 3 C 1.385198 -0.108612 -7.595450 20002 2 4 73 4 C 1.123963 -1.102110 -8.579234 20009 3 5 75 5 C 0.863466 -2.433252 -8.176489 20002 4 6 25 6 C 0.861515 -2.784286 -6.799471 20001 1 5 76 7 C 1.674909 0.638310 -5.162475 20002 2 8 72 8 C 2.409374 0.791493 -3.995053 20002 7 9 12 9 N 2.559668 2.032807 -3.447687 20002 8 10 10 C 3.282523 1.901011 -2.323878 20002 9 11 20 11 N 3.643847 0.521383 -2.090885 20002 10 12 14 12 C 3.091461 -0.221385 -3.163879 20002 8 11 13 13 O 3.191780 -1.446907 -3.324064 20006 12 14 C 4.467595 -0.119208 -0.937780 20006 11 15 71 98 15 C 3.997365 -0.216337 0.142884 20002 14 16 26 16 N 2.735860 0.221655 0.296373 20002 15 17 79 17 C 2.090153 0.180804 1.609199 20007 16 18 43 80 18 C 1.984037 1.604563 2.154295 20001 17 19 81 82 19 O 1.383838 1.633183 3.440250 20009 18 94 20 C 3.599556 3.065571 -1.539910 20002 10 21 27 21 C 2.833227 4.364367 -1.768142 20001 20 22 69 97 22 C 2.237452 5.011107 -0.507704 20009 21 23 70 96 23 C 1.865011 6.456834 -0.576498 20002 22 24 42 24 N 1.369227 7.017305 0.563700 20001 23 77 78 25 O 0.608228 -3.385039 -9.132900 20008 5 26 O 4.713328 -0.722069 1.136396 20002 15 27 N 4.553110 3.025071 -0.702565 20002 20 28 28 C 5.701151 3.603317 -0.463185 20002 27 29 30 29 O 5.682664 3.786086 0.754127 20007 28 30 C 6.872778 4.044189 -1.309536 20009 28 31 33 65 31 C 6.693646 5.514413 -1.682226 20009 30 32 66 67 32 S 8.034581 6.170017 -2.673643 20001 31 68 33 N 6.941820 3.234319 -2.521573 20002 30 34 64 34 C 7.659299 2.117949 -2.590469 20007 33 35 36 35 O 8.294530 1.667797 -1.632398 20001 34 36 C 7.647413 1.395339 -3.943763 20007 34 37 41 57 37 C 9.039836 1.531623 -4.574300 20007 36 38 58 59 38 C 9.117898 1.293351 -6.088438 20001 37 39 60 61 39 C 8.287458 0.117998 -6.555634 20015 38 40 49 40 N 7.808837 0.192389 -7.798742 20007 39 62 63 41 N 6.608656 1.941550 -4.831019 20001 36 55 56 42 O 2.007205 7.101497 -1.621382 20001 23 43 C 0.705437 -0.446003 1.468128 20002 17 44 48 44 N 0.713449 -1.740105 1.180043 20007 43 45 83 45 C -0.492284 -2.514812 0.933964 20009 44 46 50 84 46 C -0.116283 -3.969867 0.558810 20009 45 47 53 85 47 C -1.198101 -4.572065 -0.326708 20001 46 88 89 90 48 O -0.328762 0.210937 1.636028 20002 43 49 O 8.083457 -0.852453 -5.819203 20000 39 50 C -1.579338 -2.549762 2.016295 20001 45 51 52 51 O -2.609380 -3.198814 1.831173 20001 50 52 O -1.399392 -1.844428 3.212172 20001 50 95 53 C 1.222349 -3.993315 -0.198492 20001 46 54 86 87 54 C 1.241007 -3.165103 -1.480834 20007 53 91 92 93 55 H 5.966926 1.187291 -5.114175 20005 41 56 H 6.080846 2.672126 -4.332446 20005 41 57 H 7.408684 0.332164 -3.793209 20005 36 58 H 9.401532 2.551114 -4.374760 20005 37 59 H 9.651659 0.739995 -4.117140 20005 37 60 H 8.761669 2.198208 -6.602574 20005 38 61 H 10.167048 1.064966 -6.327444 20005 38 62 H 8.005370 0.989685 -8.360630 20005 40 63 H 7.255347 -0.549426 -8.163961 20005 40 64 H 6.433645 3.528482 -3.324850 20005 33 65 H 7.806053 3.916187 -0.741546 20005 30 66 H 5.757689 5.617753 -2.250824 20005 31 67 H 6.676863 6.086243 -0.742688 20005 31 68 H 9.178972 6.216096 -1.921880 20005 32 69 H 2.298758 4.556665 -2.664884 20005 21 70 H 2.362693 4.566932 0.448230 20005 22 71 H 4.776843 -1.132348 -1.006291 20005 14 72 H 1.129903 1.501971 -5.571202 20005 7 73 H 1.580139 0.888958 -7.901449 20005 3 74 H 1.122910 -2.038240 -4.796018 20005 1 75 H 1.124432 -0.846417 -9.609479 20005 4 76 H 0.666471 -3.783937 -6.500411 20005 6 77 H 1.271089 6.466796 1.386702 20005 24 78 H 1.105651 7.976719 0.572554 20005 24 79 H 2.237332 0.576270 -0.488320 20005 16 80 H 2.682543 -0.426595 2.309297 20005 17 81 H 2.993678 2.035748 2.222904 20005 18 82 H 1.351204 2.187001 1.468519 20005 18 83 H 1.591181 -2.206000 1.129534 20005 44 84 H -0.964629 -1.956780 0.112081 20005 45 85 H -0.023795 -4.557661 1.483984 20005 46 86 H 2.002968 -3.605036 0.472235 20005 53 87 H 1.392521 -5.037676 -0.499077 20005 53 88 H -1.677768 -5.411062 0.198654 20005 47 89 H -1.951985 -3.804978 -0.557442 20005 47 90 H -0.746205 -4.935411 -1.261464 20005 47 91 H 0.738289 -3.722234 -2.285123 20005 54 92 H 0.715894 -2.213683 -1.310363 20005 54 93 H 2.282527 -2.962591 -1.771050 20005 54 94 H 1.334403 2.531030 3.746726 20000 19 95 H -2.157866 -1.968974 3.770477 20000 52 96 H 1.160097 5.003378 -0.349065 0 22 97 H 3.355150 5.319202 -1.725625 0 21 98 H 5.354551 0.511008 -0.892414 0 14 $END $LINK IMOMM=.T. IQMATM(1)=20,37,19,18,5,1,2,3,4,15,71,98,14,6,72,7,12,74,11,76,10,13,9,75,8,73 $END $TINKEY parameters /home/seth/gamess/tinker/params/mm3 $END Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Computational Systems Biology Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1<>uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms ----- Original Message ----- From: Brian Salter-Duke >octa4.net.au> Date: Tuesday, January 11, 2005 9:07 am Subject: Re: CCL:GAMESS/TINKER IMOMM - $DATA needed? > On Mon, Jan 10, 2005 at 03:25:17PM +1000, Dr Seth OLSEN wrote: > > > > Dear Collegues, > > > > I'm training myself on GAMESS/TINKER. The cyclopentene test jobs > that are > > found in the documentation by Cheol Ho Choi run fine on my > installation, so > > I have tried to work up my own input for a short peptide with a > modified AA > > in the quantum region. When I attempt to run it, GAMESS > terminates an error > > saying that no $DATA group was found. However, the documentation > states that > > if all the coordinates are to be given in the $TINKEY field for > an IMOMM job > > than no $DATA group should be necessary. Moreover, the > cyclopentene IMOMM > > job with the commented-out $DATA field works fine. Can anyone > tell me what > > is going wrong. My input deck follows: > > Seth, > > Is this really your input deck? There must be a space before every > control work and before $END. Your deck is all comment - no data at > all. > Cheers, Brian. > > > $CNTRL SCFTYP=RHF RUNTYP=optimize MULT=1 EXETYP=RUN COORD=TINKER > ICHARGE=-1 > > NZVAR=288 $END > > $BASIS GBASIS=sto NGAUSS=3 $END > > $ZMAT DLC=.T. AUTO=.T. $END > > $TINXYZ > > 98 molden generated tinker .xyz (mm3 param.) > > 1 N 2.559668 2.032808 -3.447687 9 2 5 > > 2 C 2.409374 0.791493 -3.995053 2 1 3 > 6 > > 3 C 3.091461 -0.221384 -3.163879 2 2 4 14 > > 4 N 3.643847 0.521384 -2.090885 9 3 5 15 > > 5 C 3.282523 1.901012 -2.323878 2 1 4 18 > > 6 C 1.674909 0.638310 -5.162475 1 2 7 72 > > 7 C 1.390048 -0.427314 -6.208361 2 6 8 12 > > 8 C 1.385198 -0.108612 -7.595450 2 7 9 73 > > 9 C 1.123963 -1.102110 -8.579234 2 8 10 75 > > 10 C 0.863466 -2.433252 -8.176489 2 9 11 13 > > 11 C 0.861515 -2.784286 -6.799471 2 10 12 76 > > 12 C 1.124320 -1.779122 -5.825405 2 7 11 74 > > 13 O 0.608228 -3.385039 -9.132900 6 10 > > 14 O 3.191780 -1.446907 -3.324064 6 3 > > 15 C 4.467595 -0.119207 -0.937780 2 4 16 > 71 98 > > 16 C 3.997365 -0.216336 0.142884 2 15 17 31 > > 17 O 4.713328 -0.722068 1.136396 7 16 > > 18 C 3.599556 3.065572 -1.539910 1 5 19 26 > > 19 N 4.553110 3.025072 -0.702565 9 18 20 > > 20 C 5.684243 3.302363 -0.108162 2 19 21 37 > > 21 C 7.092847 3.591389 -0.572584 1 20 22 > 38 65 > > 22 N 7.327498 2.960719 -1.867530 9 21 23 64 > > 23 C 7.830224 1.735879 -1.980832 2 22 24 40 > > 24 C 8.039690 1.226535 -3.412755 1 23 25 > 41 57 > > 25 N 7.377170 2.101644 -4.392468 8 24 55 56 > > 26 C 2.833227 4.364368 -1.768142 2 18 27 > 69 97 > > 27 C 2.237451 5.011108 -0.507705 2 26 28 > 70 96 > > 28 C 1.865011 6.456835 -0.576499 2 27 29 30 > > 29 O 2.007205 7.101498 -1.621383 7 28 > > 30 N 1.369226 7.017306 0.563699 9 28 77 78 > > 31 N 2.735860 0.221656 0.296373 9 16 32 79 > > 32 C 2.090153 0.180805 1.609199 1 31 33 > 35 80 > > 33 C 0.705437 -0.446002 1.468128 2 32 34 46 > > 34 O -0.328762 0.210937 1.636028 7 33 > > 35 C 1.984037 1.604564 2.154295 1 32 36 > 81 82 > > 36 O 1.383837 1.633184 3.440250 7 35 94 > > 37 O 5.385773 3.315266 1.086135 7 20 > > 38 C 7.277566 5.102506 -0.694850 1 21 39 > 66 67 > > 39 S 8.922188 5.582399 -1.219971 15 38 68 > > 40 O 8.108043 1.031231 -1.005976 7 23 > > 41 C 9.548903 1.143626 -3.678073 1 24 42 > 58 59 > > 42 C 9.970547 1.105082 -5.153271 1 41 43 > 60 61 > > 43 C 9.094567 0.213307 -6.005771 2 42 44 45 > > 44 O 8.540316 -0.781940 -5.528265 7 43 > > 45 N 8.972657 0.560148 -7.288256 9 43 62 63 > > 46 N 0.713449 -1.740104 1.180043 9 33 47 83 > > 47 C -0.492284 -2.514811 0.933964 1 46 48 > 50 84 > > 48 C -1.579338 -2.549761 2.016295 2 47 49 54 > > 49 O -1.399392 -1.844427 3.212172 0 48 95 > > 50 C -0.116283 -3.969867 0.558810 1 47 51 > 53 85 > > 51 C 1.222349 -3.993314 -0.198492 1 50 52 > 86 87 > > 52 C 1.241007 -3.165103 -1.480834 1 51 91 > 92 93 > > 53 C -1.198101 -4.572065 -0.326708 1 50 88 > 89 90 > > 54 O -2.609380 -3.198813 1.831173 7 48 > > 55 H 6.707356 1.550632 -4.948018 5 25 > > 56 H 6.876161 2.853334 -3.897643 5 25 > > 57 H 7.586799 0.229924 -3.520723 5 24 > > 58 H 10.020885 2.023145 -3.215816 5 41 > > 59 H 9.873152 0.183037 -3.251307 5 41 > > 60 H 9.923758 2.127612 -5.556067 5 42 > > 61 H 10.988634 0.690100 -5.189157 5 42 > > 62 H 9.444407 1.365605 -7.632806 5 45 > > 63 H 8.409984 0.013364 -7.900181 5 45 > > 64 H 7.103100 3.465759 -2.694940 5 22 > > 65 H 7.810952 3.187315 0.156146 5 21 > > 66 H 6.552723 5.483409 -1.429367 5 38 > > 67 H 7.120716 5.529345 0.306753 5 38 > > 68 H 9.824291 5.275534 -0.235621 5 39 > > 69 H 2.298758 4.556666 -2.664884 5 26 > > 70 H 2.362692 4.566933 0.448229 5 27 > > 71 H 4.776843 -1.132347 -1.006291 5 15 > > 72 H 1.129903 1.501971 -5.571202 5 6 > > 73 H 1.580139 0.888958 -7.901449 5 8 > > 74 H 1.122910 -2.038240 -4.796018 5 12 > > 75 H 1.124432 -0.846417 -9.609479 5 9 > > 76 H 0.666471 -3.783937 -6.500411 5 11 > > 77 H 1.271088 6.466797 1.386701 5 30 > > 78 H 1.105651 7.976720 0.572553 5 30 > > 79 H 2.237332 0.576271 -0.488320 5 31 > > 80 H 2.682543 -0.426594 2.309297 5 32 > > 81 H 2.993677 2.035749 2.222904 5 35 > > 82 H 1.351203 2.187002 1.468519 5 35 > > 83 H 1.591181 -2.205999 1.129534 5 46 > > 84 H -0.964629 -1.956780 0.112081 5 47 > > 85 H -0.023795 -4.557660 1.483984 5 50 > > 86 H 2.002968 -3.605035 0.472235 5 51 > > 87 H 1.392521 -5.037675 -0.499077 5 51 > > 88 H -1.677768 -5.411062 0.198654 5 53 > > 89 H -1.951985 -3.804978 -0.557442 5 53 > > 90 H -0.746205 -4.935411 -1.261464 5 53 > > 91 H 0.738289 -3.722234 -2.285123 5 52 > > 92 H 0.715894 -2.213683 -1.310363 5 52 > > 93 H 2.282527 -2.962591 -1.771050 5 52 > > 94 H 1.334402 2.531031 3.746726 0 36 > > 95 H -2.157866 -1.968973 3.770477 0 49 > > 96 H 1.160096 5.003379 -0.349066 20000 27 > > 97 H 3.355150 5.319203 -1.725626 20000 26 > > 98 H 5.354551 0.511009 -0.892414 20000 15 > > $END > > $LINK > > IMOMM=.T. > > > IQMATM=20,37,19,18,5,1,2,3,4,15,71,98,14,6,72,7,12,74,11,76,10,13,9,75,8,73> LINKGE=15,16, 20,21, 18,26 > > $END > > $TINKEY > > parameters /home/seth/gamess/tinker/params/mm3 > > $END > > > > > > Cheers, > > > > Seth Olsen > > > > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > > > > Dr Seth Olsen, PhD > > Postdoctoral Fellow, Computational Systems Biology Group > > Centre for Computational Molecular Science > > Chemistry Building, > > The University of Queensland > > Qld 4072, Brisbane, Australia > > > > tel (617) 33653732 > > fax (617) 33654623 > > email: s.olsen1<>uq.edu.au > > Web: www.ccms.uq.edu.au > > > > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > > > > > > > > > > > > > > -= This is automatically added to each message by the mailing > script =- > > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > > and send your message to: CHEMISTRY<>ccl.net > > > > Send your subscription/unsubscription requests to: CHEMISTRY- > REQUEST<>ccl.net > > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > > > If your mail is bouncing from CCL.NET domain send it to the > maintainer:> Jan Labanowski, jlabanow<>nd.edu (read about it on CCL > Home Page) > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+-+ > > > > > > > > > > -- > Brian Salter-Duke (Brian Duke) b_duke<>octa4.net.au > Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia > Phone 03-92992847. http://members.iinet.net.au/~linden1/brian/ >