From chemistry-request@server.ccl.net Fri Apr 26 01:56:41 2002 Received: from hotmail.com ([64.4.37.214]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3Q5ufA28391 for ; Fri, 26 Apr 2002 01:56:41 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 25 Apr 2002 22:56:30 -0700 Received: from 171.64.127.133 by pv2fd.pav2.hotmail.msn.com with HTTP; Fri, 26 Apr 2002 05:56:30 GMT X-Originating-IP: [171.64.127.133] From: "Bin Shan" To: chemistry@ccl.net Subject: why I could not get convergence even on the initial guess? Date: Fri, 26 Apr 2002 05:56:30 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 26 Apr 2002 05:56:30.0593 (UTC) FILETIME=[1CAF3710:01C1ECE7] I am calculating a system consists of 3 gold atoms and 1 sulfer atom.(originally,there should be more carbon and hydrgon to follow,but since I can not even get convergence on this simple system,I didn't go further.)I am using a LANL2DZ basis set for 3 gold atoms and 6-31G(d) for sulfer atoms.(I have tried adding SCF(MaxCyc=200),still doesn't work)However,the job terminates with the following error:(I am using Gaussian98RevA.11.2)Anyone has any idea what is wrong?help me out,please! ....... of initial guess= 0.7500 Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Virtual orbitals will be shifted by 0.200 hartree. Defaulting to unpruned grid for atomic number 79. Restarting incremental Fock formation. Restarting incremental Fock formation. Restarting incremental Fock formation. >>>>>>>>>> Convergence criterion not met. SCF Done: E(UB+HF-LYP) = -804.520113362 A.U. after 65 cycles Convg = 0.8395D-06 -V/T = 2.5258 S**2 = 0.7554 Annihilation of the first spin contaminant: S**2 before annihilation 0.7554, after 0.7500 Convergence failure -- run terminated. Error termination via Lnk1e in /afs/ir.stanford.edu/class/chemeng444a/programs/gaussian/sun4x_58/g98/l502.exe. Job cpu time: 0 days 0 hours 27 minutes 37.1 seconds. Here is my input file. #gfinput iop(6/7=3) # b3lyp/gen opt(modredundant,maxcycle=200) Pseudo=Read Title Card Required 0 2 Au Au 1 2.884000 Au 1 2.884331 2 60.003801 S 3 2.108711 1 46.856789 2 57.247633 1 B 2 B 3 B * F Au 0 LANL2DZ **** 4 0 6-31g(d) **** Au 0 LANL2DZ _________________________________________________________________ Send and receive Hotmail on your mobile device: http://mobile.msn.com From chemistry-request@server.ccl.net Fri Apr 26 11:06:56 2002 Received: from ned1.sims.nrc.ca ([132.246.108.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3QF6uA05047 for ; Fri, 26 Apr 2002 11:06:56 -0400 Received: from localhost (ps@localhost) by ned1.sims.nrc.ca (8.8.8/8.8.8) with ESMTP id LAA18407; Fri, 26 Apr 2002 11:06:38 -0400 (EDT) Date: Fri, 26 Apr 2002 11:06:38 -0400 From: Serguei Patchkovskii Reply-To: Serguei.Patchkovskii@nrc.ca To: uccajgo7@netscape.net cc: chemistry@ccl.net Subject: Re: CCL:DeMon NMR In-Reply-To: <1A661AF6.05B85BDF.00A8F98F@netscape.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Jorge, You should send deMon support questions to deMon technical contact at deMonkey@deMon-software.com (pronounced "deMon-key", and NOT "de Monkey" ;-)). You can also try sending deMon-related questions to the deMon users mailing list, at deMon-users@deMon-software.com. In order to be able to help you, I will need to see the complete input and output files, as well as the operating system and compiler versions. Sincerely yours, Serguei On Thu, 25 Apr 2002 uccajgo7@netscape.net wrote: > I am running a DeMonNMR calculation to predict the 3JHC in a compound with a > sulfur atom with a positive charge.Can someone suggest me an > Orbital/Auxiliary basis set for that? I am trying the iii_iglo and ii3_iglo > and I am having travels. > Thanks > Jorge --- Dr. Serguei Patchkovskii Tel: +1-(613)-991-2719 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii@nrc.ca Research Council Officer Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2158, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From chemistry-request@server.ccl.net Fri Apr 26 03:33:27 2002 Received: from web14913.mail.yahoo.com ([216.136.225.240]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g3Q7XQA29355 for ; Fri, 26 Apr 2002 03:33:27 -0400 Message-ID: <20020426073316.51271.qmail@web14913.mail.yahoo.com> Received: from [161.142.10.27] by web14913.mail.yahoo.com via HTTP; Fri, 26 Apr 2002 00:33:16 PDT Date: Fri, 26 Apr 2002 00:33:16 -0700 (PDT) From: Ng Pei Ling Subject: .dlg file in autodock To: CHEMISTRY@ccl.net MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="0-518000143-1019806396=:50528" --0-518000143-1019806396=:50528 Content-Type: multipart/alternative; boundary="0-2038914912-1019806396=:50528" --0-2038914912-1019806396=:50528 Content-Type: text/plain; charset=us-ascii To my friends : For the attached file : 1. Is the mean dock energy too high for enzyme 2hck dock with quercetin(ligand) ? The lowest dock energy is -6.77. 2. What is the mean of 32 for the number of cluster ? It is mean there are 32 suitable conformation for docking? 3. What should I change in the input file to get lower docked energy? Thanks for yours help. Miss Ng Pei Ling School of Pharmaceutical Sciences, University Sciences Malaysia, Minden 11800, Penang, Malaysia. Tel:604-6577888 Fax:604-6570017 --------------------------------- Do You Yahoo!? Yahoo! Games - play chess, backgammon, pool and more --0-2038914912-1019806396=:50528 Content-Type: text/html; charset=us-ascii

To my friends :

   For the attached file :

  1. Is the mean dock energy too high for enzyme 2hck dock with quercetin(ligand) ? The lowest dock energy is -6.77.

  2. What is the mean of 32 for the number of cluster ? It is mean there are 32 suitable conformation for docking?

  3. What should I change in the input file to get lower docked energy?

 

 

Thanks for yours help.



Miss Ng Pei Ling
School of Pharmaceutical Sciences,

University Sciences Malaysia,

Minden 11800, Penang, Malaysia.

Tel:604-6577888
Fax:604-6570017


Do You Yahoo!?
Yahoo! Games - play chess, backgammon, pool and more --0-2038914912-1019806396=:50528-- --0-518000143-1019806396=:50528 Content-Type: text/plain; name=Clustering_Histogram Content-Description: Clustering_Histogram Content-Disposition: inline; filename=Clustering_Histogram CLUSTERING HISTOGRAM 2HCK (Using UNIX Command Grep -i 'atom' 2hck1.pdbq > 2hck2.pdbq followed by Grep -v 'REMARK' 2hck2.pdbq > 2hck3.pdbq) ________________________________________________________________________________ | | | | | Clus | Lowest | Run | Mean | Num | Histogram -ter | Docked | | Docked | in | Rank | Energy | | Energy | Clus| 5 10 15 20 25 30 35 _____|___________|_____|___________|_____|____:____|____:____|____:____|____:___ 1 | -6.88 | 32 | -6.77 | 2 |## 2 | -6.48 | 34 | -6.48 | 1 |# 3 | -5.97 | 99 | -5.55 | 32 |################################ 4 | -5.76 | 21 | -5.76 | 1 |# 5 | -5.61 | 68 | -5.61 | 1 |# 6 | -5.25 | 6 | -5.25 | 1 |# 7 | -4.87 | 77 | -4.80 | 2 |## 8 | -4.74 | 42 | -4.73 | 2 |## 9 | -4.70 | 46 | -4.70 | 1 |# 10 | -4.70 | 85 | -4.70 | 1 |# 11 | -4.70 | 35 | -4.55 | 4 |#### 12 | -4.69 | 53 | -4.69 | 1 |# 13 | -4.68 | 75 | -4.68 | 1 |# 14 | -4.65 | 84 | -4.65 | 1 |# 15 | -4.61 | 2 | -4.61 | 1 |# 16 | -4.58 | 27 | -4.49 | 6 |###### 17 | -4.52 | 91 | -4.47 | 2 |## 18 | -4.50 | 20 | -4.50 | 2 |## 19 | -4.47 | 86 | -4.46 | 2 |## 20 | -4.47 | 88 | -4.47 | 1 |# 21 | -4.43 | 96 | -4.37 | 5 |##### 22 | -4.42 | 36 | -4.42 | 1 |# 23 | -4.42 | 1 | -4.42 | 1 |# 24 | -4.39 | 10 | -4.35 | 2 |## 25 | -4.38 | 57 | -4.37 | 2 |## 26 | -4.36 | 38 | -4.36 | 1 |# 27 | -4.35 | 56 | -4.35 | 1 |# 28 | -4.32 | 47 | -4.32 | 1 |# 29 | -4.30 | 79 | -4.30 | 1 |# 30 | -4.27 | 14 | -4.25 | 2 |## 31 | -4.27 | 64 | -4.24 | 2 |## 32 | -4.23 | 18 | -4.23 | 1 |# 33 | -4.19 | 8 | -4.15 | 2 |## 34 | -4.18 | 61 | -4.18 | 1 |# 35 | -4.16 | 9 | -4.16 | 1 |# 36 | -4.16 | 58 | -4.16 | 1 |# 37 | -4.15 | 70 | -4.15 | 2 |## 38 | -4.14 | 65 | -4.14 | 1 |# 39 | -4.09 | 19 | -4.09 | 1 |# 40 | -3.96 | 82 | -3.96 | 1 |# 41 | -3.90 | 100 | -3.90 | 1 |# 42 | -3.85 | 28 | -3.85 | 1 |# 43 | -3.77 | 63 | -3.77 | 1 |# 44 | -3.72 | 4 | -3.72 | 1 |# 45 | -2.04 | 87 | -2.04 | 1 |# _____|___________|_____|___________|_____|______________________________________ RMSD TABLE 2HCK _____________________________________________________________________ | | | | | | Rank | Sub- | Run | Docked | Cluster | Reference | Grep | Rank | | Energy | RMSD | RMSD | Pattern _____|______|______|___________|_________|_________________|___________ 1 1 32 -6.88 0.00 137.36 RANKING 1 2 29 -6.66 0.29 137.47 RANKING 2 1 34 -6.48 0.00 137.57 RANKING 3 1 99 -5.97 0.00 133.23 RANKING 3 2 43 -5.97 0.05 133.21 RANKING 3 3 31 -5.94 0.04 133.23 RANKING 3 4 74 -5.90 0.09 133.20 RANKING 3 5 52 -5.87 0.14 133.21 RANKING 3 6 25 -5.87 0.18 133.19 RANKING 3 7 30 -5.86 0.08 133.24 RANKING 3 8 33 -5.85 0.13 133.19 RANKING 3 9 78 -5.78 0.23 133.29 RANKING 3 10 90 -5.76 0.21 133.29 RANKING 3 11 92 -5.76 0.24 133.20 RANKING 3 12 94 -5.70 0.18 133.25 RANKING 3 13 16 -5.69 0.26 133.27 RANKING 3 14 37 -5.66 0.29 133.20 RANKING 3 15 67 -5.65 0.27 133.21 RANKING 3 16 72 -5.64 0.32 133.34 RANKING 3 17 98 -5.64 0.31 133.28 RANKING 3 18 60 -5.60 0.35 133.35 RANKING 3 19 69 -5.57 0.37 133.31 RANKING 3 20 24 -5.56 0.33 133.35 RANKING 3 21 54 -5.51 0.32 133.34 RANKING 3 22 89 -5.43 0.33 133.31 RANKING 3 23 83 -5.43 0.35 133.26 RANKING 3 24 51 -5.39 0.39 133.30 RANKING 3 25 5 -5.30 0.41 133.25 RANKING 3 26 97 -5.24 0.28 133.14 RANKING 3 27 15 -5.20 0.43 133.09 RANKING 3 28 81 -5.16 0.50 133.30 RANKING 3 29 62 -5.02 0.47 133.19 RANKING 3 30 59 -4.99 0.45 133.08 RANKING 3 31 66 -4.93 0.41 133.09 RANKING 3 32 17 -4.87 0.47 133.08 RANKING 4 1 21 -5.76 0.00 137.59 RANKING 5 1 68 -5.61 0.00 133.86 RANKING 6 1 6 -5.25 0.00 133.85 RANKING 7 1 77 -4.87 0.00 132.82 RANKING 7 2 50 -4.74 0.45 132.61 RANKING 8 1 42 -4.74 0.00 131.30 RANKING 8 2 80 -4.71 0.38 131.35 RANKING 9 1 46 -4.70 0.00 133.09 RANKING 10 1 85 -4.70 0.00 132.66 RANKING 11 1 35 -4.70 0.00 133.31 RANKING 11 2 11 -4.60 0.47 133.32 RANKING 11 3 7 -4.56 0.49 133.32 RANKING 11 4 39 -4.35 0.37 133.24 RANKING 12 1 53 -4.69 0.00 131.72 RANKING 13 1 75 -4.68 0.00 132.39 RANKING 14 1 84 -4.65 0.00 131.85 RANKING 15 1 2 -4.61 0.00 132.77 RANKING 16 1 27 -4.58 0.00 130.90 RANKING 16 2 73 -4.57 0.20 130.84 RANKING 16 3 13 -4.56 0.44 131.08 RANKING 16 4 40 -4.50 0.10 130.92 RANKING 16 5 76 -4.39 0.26 130.81 RANKING 16 6 12 -4.36 0.32 130.83 RANKING 17 1 91 -4.52 0.00 132.58 RANKING 17 2 23 -4.43 0.21 132.45 RANKING 18 1 20 -4.50 0.00 138.07 RANKING 18 2 55 -4.49 0.30 138.25 RANKING 19 1 86 -4.47 0.00 133.21 RANKING 19 2 26 -4.45 0.12 133.20 RANKING 20 1 88 -4.47 0.00 133.23 RANKING 21 1 96 -4.43 0.00 133.56 RANKING 21 2 71 -4.40 0.22 133.47 RANKING 21 3 22 -4.36 0.26 133.37 RANKING 21 4 95 -4.34 0.46 133.35 RANKING 21 5 3 -4.32 0.38 133.58 RANKING 22 1 36 -4.42 0.00 133.12 RANKING 23 1 1 -4.42 0.00 132.32 RANKING 24 1 10 -4.39 0.00 133.64 RANKING 24 2 44 -4.31 0.40 133.59 RANKING 25 1 57 -4.38 0.00 133.42 RANKING 25 2 48 -4.37 0.05 133.40 RANKING 26 1 38 -4.36 0.00 132.77 RANKING 27 1 56 -4.35 0.00 132.24 RANKING 28 1 47 -4.32 0.00 132.80 RANKING 29 1 79 -4.30 0.00 131.29 RANKING 30 1 14 -4.27 0.00 132.53 RANKING 30 2 93 -4.22 0.21 132.65 RANKING 31 1 64 -4.27 0.00 133.37 RANKING 31 2 45 -4.22 0.48 133.34 RANKING 32 1 18 -4.23 0.00 137.02 RANKING 33 1 8 -4.19 0.00 133.63 RANKING 33 2 41 -4.10 0.44 133.79 RANKING 34 1 61 -4.18 0.00 138.00 RANKING 35 1 9 -4.16 0.00 133.01 RANKING 36 1 58 -4.16 0.00 138.52 RANKING 37 1 70 -4.15 0.00 132.55 RANKING 37 2 49 -4.15 0.18 132.48 RANKING 38 1 65 -4.14 0.00 133.38 RANKING 39 1 19 -4.09 0.00 134.06 RANKING 40 1 82 -3.96 0.00 130.54 RANKING 41 1 100 -3.90 0.00 133.71 RANKING 42 1 28 -3.85 0.00 133.29 RANKING 43 1 63 -3.77 0.00 131.15 RANKING 44 1 4 -3.72 0.00 131.54 RANKING 45 1 87 -2.04 0.00 133.17 RANKING _______________________________________________________________________ --0-518000143-1019806396=:50528-- From chemistry-request@server.ccl.net Fri Apr 26 05:13:04 2002 Received: from igc.phys.chem.ethz.ch ([129.132.218.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3Q9D3A30826 for ; Fri, 26 Apr 2002 05:13:04 -0400 Received: from humagne.ethz.ch (humagne [129.132.218.162]) by igc.phys.chem.ethz.ch (8.11.4/8.11.4) with ESMTP id g3Q9Crx07694 for ; Fri, 26 Apr 2002 11:12:53 +0200 (MEST) Received: (from portmann@localhost) by humagne.ethz.ch (8.11.4/8.11.4) id g3Q9CrX09483 for chemistry@ccl.net; Fri, 26 Apr 2002 11:12:53 +0200 (MEST) Date: Fri, 26 Apr 2002 11:12:53 +0200 (MEST) Message-Id: <200204260912.g3Q9CrX09483@humagne.ethz.ch> From: Stefan Portmann Reply-To: info@watoc02.ch Subject: WATOC'02: Early Bird Discount! Content-Type: text Dear Madam or Sir 6th WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS (WATOC'02) August 4-9, 2002, Palazzo dei Congressi, Lugano, Switzerland Theory, Computation and Information Science in Chemistry, Biochemistry and Materials Science Don't miss the opportunity to get the early bird discount (Deadline: April 30 2002) and register immediately at http://www.watoc02.ch Please also have a look at the information regarding local expenses in the section "Budgetary Considerations". We offer low cost housing possibilities, check it out! A first detailed program is also available. Abstracts for poster presentations can still be submitted. In order to give the poster sessions optimal visibility, an award program was established. The posters will be rated both on popular and on jury votes. There will be a two hour award ceremony on Thursday evening. The poster sessions will be endowed by Gaussian, Inc.. We are looking forward to see you in Lugano. Hans Peter Luethi and Stefan Portmann ETH Zurich From chemistry-request@server.ccl.net Fri Apr 26 11:17:07 2002 Received: from euch4e.chem.emory.edu ([170.140.59.12]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3QFH7A05627 for ; Fri, 26 Apr 2002 11:17:07 -0400 Received: from localhost (guishan@localhost) by euch4e.chem.emory.edu (AIX4.3/8.9.3/8.9.3) with ESMTP id LAA38292 for ; Fri, 26 Apr 2002 11:16:50 -0400 Date: Fri, 26 Apr 2002 11:16:50 -0400 (EDT) From: Guishan Zheng To: Subject: How to "loose" molecular symmetry in MOPAC2002 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, all I am running a optimization job of C240 using MOPAC2002. The output file shows that this molecule is of symmetry C1, how can I run it at a higher symmetry, like Ih. When I did the same job with Gaussian, I can add the keyword "symm=loose", but how can I do with MOPAC? Any help are greatly appreciated. Thanks in advance. Have a nice day. Guishan Zheng From chemistry-request@server.ccl.net Fri Apr 26 12:13:56 2002 Received: from postal.ucc.uno.edu ([137.30.1.80]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3QGDoA07034 for ; Fri, 26 Apr 2002 12:13:52 -0400 Received: from CONVERSION-DAEMON by postal.ucc.uno.edu (PMDF V5.2-32 #38784) id <0GV600401NODPM@postal.ucc.uno.edu> for chemistry@ccl.net; Fri, 26 Apr 2002 11:13:05 -0500 (CDT) Received: from uno.edu (acad-2-1-066.dhcp.uno.edu [137.30.117.66]) by postal.ucc.uno.edu (PMDF V5.2-32 #38784) with ESMTP id <0GV6005BPNNRXB@postal.ucc.uno.edu> for chemistry@ccl.net; Fri, 26 Apr 2002 11:11:51 -0500 (CDT) Date: Fri, 26 Apr 2002 11:05:17 -0500 From: "Monica C. Concha" Subject: Help To: "chemistry@ccl.net" Message-id: <3CC97ABA.52265D57@uno.edu> Organization: University of New Orleans MIME-version: 1.0 X-Mailer: Mozilla 4.73 (Macintosh; U; PPC) Content-type: MULTIPART/MIXED; BOUNDARY="Boundary_(ID_geIL7cYCYOyKwD7FcrVKwQ)" X-Accept-Language: en,pdf This is a multi-part message in MIME format. --Boundary_(ID_geIL7cYCYOyKwD7FcrVKwQ) Content-type: text/plain; charset=iso-8859-1; x-mac-type=54455854; x-mac-creator=4D4F5353 Content-transfer-encoding: 8BIT Dear CCLers, I was trying to run a job using cbs-qb3 (gaussian 98 A.7) and it crashed at the very last steps of cbsextrap due to lack of space. When I try to restart it with the opt(restart) option it is able to read in info > from the checkpoint file but it crashed in L401 Iop(5). Is there some way to get around this problem without having to repeat the entire calculation. The Gaussian manual says that cbs jobs are restartable but noone in my group has been able to do this. Any suggestions? Thanks Mónica -- Monica C. Concha Research Associate Dept. Of Chemistry University of New Orleans New Orleans LA 70148 E-mail mconcha@uno.edu --Boundary_(ID_geIL7cYCYOyKwD7FcrVKwQ) Content-type: text/x-vcard; charset=us-ascii; name=mconcha.vcf Content-description: Card for Monica C. Concha Content-disposition: attachment; filename=mconcha.vcf Content-transfer-encoding: 7BIT begin:vcard n:Concha;Monica C. tel;fax:504-280-6860 tel;home:504- 456-2325 tel;work:504-280-7216 x-mozilla-html:FALSE org:University of New Orleans;Chemistry adr:;;Lakeshore;New Orleans;LA;70148;USA version:2.1 email;internet:mconcha@uno.edu title:Research Associate x-mozilla-cpt:;1 fn:Monica C. Concha end:vcard --Boundary_(ID_geIL7cYCYOyKwD7FcrVKwQ)-- From chemistry-request@server.ccl.net Fri Apr 26 12:28:50 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3QGSoA07480 for ; Fri, 26 Apr 2002 12:28:50 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id MAA72793; Fri, 26 Apr 2002 12:21:57 -0400 (EDT) Date: Fri, 26 Apr 2002 12:21:56 -0400 From: Rick Venable To: "J. Zheng" cc: chemistry@ccl.net, Goran Widmalm Subject: Re: CCL:ask for workshop of charmm or linux cluster. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 24 Apr 2002, J. Zheng wrote: > hi, my question is a little bit out of subject of this forum. Now, I > am working on how to write a script by using CHARMM software > package. It really takes me lots of time to learn how to use it. I > am wondering that if there is any workshop for teaching how to use > CHARMM. I think it would be much better for me in order to save the > time and learn more stuff from CHARMM. CHARMM related mailing lists: charmm-bbs@csir.org To subscribe, send email to sympa@csir.org with the text subscribe charmm-bbs in the message body; sympa is an automated list manager. charmm-users@tammy.harvard.edu To subscribe, send email to chmgr@tammy.harvard.edu and indicate that you wish to receive 'charmm-users' messages; not automated. CHARMM related web sites: HTML versions of .doc files: www.lobos.nih.gov/Charmm www.scripps.edu/brooks/charmm_docs/charmm.html Tutorial: www.psc.edu/general/software/packages/charmm/charmm.html =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Fri Apr 26 15:37:40 2002 Received: from smtp.unc.edu ([152.2.1.241]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3QJbZA10729 for ; Fri, 26 Apr 2002 15:37:39 -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 g3QJatQ1006114; Fri, 26 Apr 2002 15:36:55 -0400 (EDT) Sender: jochen@bock.chem.unc.edu To: molpro-user Cc: chemistry@ccl.net Subject: molpro-parser User-Agent: XEmacs/Gnus X-Attribution: Jochen X-Face: -%Z4EZ6iY'4m:wiK:!v Organization: University of North Carolina Date: 26 Apr 2002 15:36:55 -0400 Message-ID: Lines: 22 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii I got tired of retyping my grep-regexps and struggling with multiline matches again and again, so I wrote a small python script 'molpro-parser' to extract information from molpro output files. Currently it supports extracting energies, rotational constants, and variable sections of geometry optimizations. It can operate on multiple files at once and can be used as a stdin--stdout filter. The script is available at ,---- | http://python.jochen-kuepper.de/jkext `---- Feel free to send comments, suggestions, patches, or simply snippets of output files you would like the script to extract. 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 From chemistry-request@server.ccl.net Fri Apr 26 15:52:04 2002 Received: from aspx-smtp.netaspx.com ([137.66.136.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3QJq3A10943 for ; Fri, 26 Apr 2002 15:52:03 -0400 Received: from aspx-mail.netaspx.com ([137.66.136.3]) by aspx-smtp.netaspx.com (Lotus Domino Release 5.0.9) with SMTP id 2002042614514624:116084 ; Fri, 26 Apr 2002 14:51:46 -0500 To: chemistry@ccl.net Subject: Locating a transition state X-Mailer: Lotus Notes Release 5.0.4a July 24, 2000 From: Genzo.Tanaka@netaspx.com Message-ID: Date: Fri, 26 Apr 2002 15:51:46 -0400 X-MIMETrack: Serialize by Router on ASPX-Mail/netASPx(Release 5.0.6a |January 17, 2001) at 04/26/2002 02:51:48 PM, Serialize complete at 04/26/2002 02:51:48 PM, Itemize by SMTP Server on ASPX-SMTP/netASPx(Release 5.0.9 |November 16, 2001) at 04/26/2002 02:51:46 PM, Serialize by Router on ASPX-SMTP/netASPx(Release 5.0.9 |November 16, 2001) at 04/26/2002 02:51:55 PM, Serialize complete at 04/26/2002 02:51:55 PM MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_alternative 006D1DB085256BA7_=" This is a multipart message in MIME format. --=_alternative 006D1DB085256BA7_= Content-Type: text/plain; charset="us-ascii" 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 --=_alternative 006D1DB085256BA7_= Content-Type: text/html; charset="us-ascii"
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
  --=_alternative 006D1DB085256BA7_=--