From owner-chemistry@ccl.net Wed Mar 21 00:32:01 2007 From: "Soren Eustis soren/a\jhu.edu" To: CCL Subject: CCL:G: General Molecule/Fragment Database Message-Id: <-33860-070321002132-11599-o+NvvOKiLTeair8dvFt/Jg-$-server.ccl.net> X-Original-From: "Soren Eustis" Content-language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_00A1_01C76B46.71BD90C0" Date: Tue, 20 Mar 2007 23:21:09 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren(0)jhu.edu] This is a multipart message in MIME format. ------=_NextPart_000_00A1_01C76B46.71BD90C0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I am looking for a general molecule/fragment database in .pdb or .mol (.frg?) format that could be used to help expedite the preparation of runs in Gaussian. This may even be useful as a thought/research tool, simply having 3D structures to manipulate could be quite useful. I am sure there are some good options out there. Anyone have any suggestions (freeware preferred, but I am amenable to paying a few dollars as well.) Regards, Soren Soren N. Eustis Graduate Research Assistant Department of Chemistry Johns Hopkins University 3400 N. Charles Street Baltimore, MD 21218 (410) 516-4675 (office) (410) 925-5167 (cell) (410) 516-8420 (fax) soren]|[jhu.edu ------=_NextPart_000_00A1_01C76B46.71BD90C0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I am looking for a general molecule/fragment = database in .pdb or .mol (.frg?) format that could be used to help expedite the = preparation of runs in Gaussian. This may even be useful as a thought/research = tool, simply having 3D structures to manipulate could be quite useful. I = am sure there are some good options out there. Anyone have any suggestions = (freeware preferred, but I am amenable to paying a few dollars as = well.)

Regards,

Soren

Soren N. Eustis

Graduate Research Assistant

Department of Chemistry

Johns Hopkins University

3400 N. Charles Street

Baltimore, MD 21218

(410) 516-4675 (office)

(410) 925-5167 (cell)

(410) 516-8420 (fax)

soren]|[jhu.edu

------=_NextPart_000_00A1_01C76B46.71BD90C0-- From owner-chemistry@ccl.net Wed Mar 21 02:24:01 2007 From: "Seth Olsen s.olsen1-#-uq.edu.au" To: CCL Subject: CCL: Implementation of Freed's Effective Valence Shell Hamiltonian? Message-Id: <-33861-070321000250-9684-z0lVAhkLMUy769J+MWtl3g{=}server.ccl.net> X-Original-From: Seth Olsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 21 Mar 2007 13:04:35 +1000 MIME-Version: 1.0 Sent to CCL by: Seth Olsen [s.olsen1{=}uq.edu.au] Hi CCL, I was curious to find out if any proprietary or open-source quantum chemistry program includes an implementation of Karl Freed's effective valence shell hamiltonian (Hv) method? Cheers, Seth From owner-chemistry@ccl.net Wed Mar 21 08:42:01 2007 From: "alessandro casoni alessandro.casoni ~ studenti.unimi.it" To: CCL Subject: CCL: Protein Morpher Message-Id: <-33862-070321055603-23917-JGj5HfGv+yLniDk1Dz+23g^server.ccl.net> X-Original-From: alessandro casoni Content-transfer-encoding: 8BIT Content-type: text/plain; charset=UTF-8 Date: Wed, 21 Mar 2007 10:13:16 +0100 MIME-version: 1.0 Sent to CCL by: alessandro casoni [alessandro.casoni_._studenti.unimi.it] Thanks to Samuel, Warren and Nathalie for the useful answers. I'm going to use Yale Morph Server and WEBnma... Cheers Alessandro -- Dr. Alessandro Casoni Istituto di Chimica Organica "A. Marchesini" Università degli Studi di Milano - Facoltà di Farmacia Via G. Venezian 21, 20133 Milano E-Mail: alessandro.casoni _ unimi.it Tel. +390250314480 FAX +390250314476 From owner-chemistry@ccl.net Wed Mar 21 09:43:01 2007 From: "Nathalie Reuter nathalie.reuter###cbu.uib.no" To: CCL Subject: CCL: Protein Morpher Message-Id: <-33863-070321051430-19708-9bHQKiKnxaxs9IAH+ps3oQ-x-server.ccl.net> X-Original-From: Nathalie Reuter Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 21 Mar 2007 09:42:43 +0100 MIME-Version: 1.0 Sent to CCL by: Nathalie Reuter [nathalie.reuter/./cbu.uib.no] Hi, you can try WEBnma (http://www.bioinfo.no/tools/normalmodes). If you first upload the open conformation, calculate the approx. normal modes and then choose the option 'calculate animation of a transconformation' at the bottom of the analysis page. You need then to upload the second (close) conformation. I would be pleased to help you do it if you encounter problems with our website. Regards, Nathalie --- Nathalie Reuter Computational Biology Unit Univ. of Bergen Norway http://www.cbu.uib.no http://www.bioinfo.no Alessandro Casoni alessandro.casoni a unimi.it wrote: > Sent to CCL by: "Alessandro Casoni" [alessandro.casoni!A!unimi.it] > Hi, does anyone know any software (preferably open source) able to do protein morphing? I have a receptor in 2 conformations and I want to build an intermediate conformation. > > Any help will be appreciated... > > Alessandro> > > > From owner-chemistry@ccl.net Wed Mar 21 15:41:01 2007 From: "Julia Subbotina ysubboti() ucalgary.ca" To: CCL Subject: CCL: ccsd(t) disc requirements Message-Id: <-33864-070321143839-28874-S1sQQce0T8Zp8BRk/PXGFg]-[server.ccl.net> X-Original-From: "Julia Subbotina" Date: Wed, 21 Mar 2007 14:38:35 -0400 Sent to CCL by: "Julia Subbotina" [ysubboti%a%ucalgary.ca] Dear CCLers I have a problem with running CCSD(T)\ Ahlrichs pVDZ single point energy job. I am limited with my disc space (~110GB), but this job seems to need even more (Transformation cannot fit in the specified MaxDisk.). The input line is: %mem=3GB ccsd(t)/gen MaxDisk=100GB And later I am expected to make a single point calculation for the bigger system than one I am struggling with now. I need a suggestion how i can handle this kind of problem. Any tips are welcome. Thank you in advance, Julia From owner-chemistry@ccl.net Wed Mar 21 17:50:01 2007 From: "tlazza##po-box.mcgill.ca" To: CCL Subject: CCL:G: Amber in Gaussian, Help? Message-Id: <-33865-070321112029-4216-FWMCCfQjw99NiXxqmOuQ6g[]server.ccl.net> X-Original-From: tlazza]^[po-box.mcgill.ca Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Wed, 21 Mar 2007 10:32:14 -0400 MIME-Version: 1.0 Sent to CCL by: tlazza|-|po-box.mcgill.ca Dear CCL people, I have a question concerning the use of AMBER in Gaussian 03. I am modeling a polymer of styrene and maleic anhydride. Gaussian runs fine when optimizing the styrene part of the polymer but fails when adding maleic anhydride (5 member ring with 4 carbons and 1 oxygen, and 2 C=O bonds) I believe it has something to do with missing parameters. Could anyone enlighten me on this problem and maybe suggest how to solve it. I would greatly apreciate any help. The output file for maleic anhydride fails with amber and reads as such: # opt amber geom=connectivity ----------------------------- 1/6=10,10=10,14=-1,18=4000020,38=1,56=2,57=2,64=3/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=2,7=1,11=9,16=1,25=1,30=1/1; 4/20=11,22=1001,24=3/2; 7/44=-1/16; 1/6=10,10=10,14=-1,18=4000020,64=3/3(1); 99//99; 2/9=110/2; 3/5=2,7=1,11=9,16=1,25=1,30=1/1; 4/16=2,20=11,22=1001,24=3/2; 7/44=-1/16; 1/6=10,10=10,14=-1,18=4000020,64=3/3(-4); 2/9=110/2; 99//99; ----- test7 ----- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C-CT- H-HC- 1 B1 H-HC- 1 B2 2 A1 C-CT- 1 B3 3 A2 2 D1 0 H-HC- 4 B4 1 A3 3 D2 0 H-HC- 4 B5 1 A4 3 D3 0 C-CA- 1 B6 4 A5 5 D4 0 C-CA- 4 B7 1 A6 7 D5 0 O-O2- 7 B8 1 A7 4 D6 0 O-O2- 8 B9 4 A8 1 D7 0 O-O2- 7 B10 1 A9 4 D8 0 Variables: B1 1.07 B2 1.07 B3 1.51674 B4 1.07 B5 1.07 B6 1.53548 B7 1.52063 B8 1.3013 B9 1.3013 B10 1.33149 A1 108.27071 A2 112.26108 A3 111.65225 A4 112.62779 A5 100.98759 A6 99.96086 A7 125.11583 A8 126.18119 A9 109.75626 D1 -123.43758 D2 -43.6756 D3 78.18336 D4 79.94422 D5 -34.62622 D6 -149.9875 D7 -150.53131 D8 30.81761 I= 7 IAn= 6 Valence= 6. JB= 1 J= 9 IAn= 8 IBT= 2 Dist= 1.30D+00 JB= 2 J= 11 IAn= 8 IBT= 1 Dist= 1.33D+00 JB= 3 J= 1 IAn= 6 IBT= 1 Dist= 1.54D+00 I= 8 IAn= 6 Valence= 6. JB= 1 J= 10 IAn= 8 IBT= 2 Dist= 1.30D+00 JB= 2 J= 11 IAn= 8 IBT= 1 Dist= 1.45D+00 JB= 3 J= 4 IAn= 6 IBT= 1 Dist= 1.52D+00 Include all MM classes Bondstretch undefined between atoms 7 9 Bondstretch undefined between atoms 7 11 Bondstretch undefined between atoms 8 10 Bondstretch undefined between atoms 8 11 Angle bend undefined between atoms 1 7 9 Angle bend undefined between atoms 1 7 11 Angle bend undefined between atoms 4 8 10 Angle bend undefined between atoms 4 8 11 Angle bend undefined between atoms 7 11 8 Angle bend undefined between atoms 9 7 11 Angle bend undefined between atoms 10 8 11 MM function not complete Error termination via Lnk1e in C:\G03W\l101.exe at Tue Mar 20 21:20:34 2007. Job cpu time: 0 days 0 hours 0 minutes 3.0 seconds. File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 1 Scr= 1 Thomas D. Lazzara From owner-chemistry@ccl.net Wed Mar 21 19:00:01 2007 From: "Noel M. O Boyle baoilleach###gmail.com" To: CCL Subject: CCL:G: ANN: cclib 0.7 released Message-Id: <-33867-070321180136-11311-GlsgmZP61MsfsHAvndXyEw^server.ccl.net> X-Original-From: "Noel M. O Boyle" Date: Wed, 21 Mar 2007 18:01:33 -0400 Sent to CCL by: "Noel M. O Boyle" [baoilleach(-)gmail.com] cclib 0.7 is now available for download from http://cclib.sf.net. cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, GAMESS (US), GAMESS-UK, Gaussian, Jaguar and PC GAMESS. The main new features in this release are: * a Jaguar parser * cclib now extracts the Gaussian basis, the MP-corrected energies, and the Cartesian displacement vectors * Charge Decomposition Analysis, Fragment analysis For more details, see http://cclib.sf.net/wiki/index.php/Changelog Among other data, cclib extracts: * coordinates * atomic orbital information * molecular orbital information * information on vibrational modes * the results of a TD-DFT calculation (For a complete list see http://cclib.sf.net/wiki/index.php/Parsed_Data). cclib also provides some calculation methods for interpreting some electronic properties of molecules using analyses such as: * Mulliken population analysis * Overlap population analysis * Calculation of Mayer's bond orders. For information on how to use cclib, see http://cclib.sf.net/wiki/index.php/Using_cclib. If you need help, find a bug, want new features or have any questions, please send an email to our mailing list: cclib-users{=}lists.sourceforge.net Regards, The cclib development team From owner-chemistry@ccl.net Wed Mar 21 20:08:01 2007 From: "Gregory Sandala sandala!=!chem.usyd.edu.au" To: CCL Subject: CCL:G: ccsd(t) disc requirements Message-Id: <-33868-070321192039-12154-gVcmctjJCAqJ8yt20fhfmA++server.ccl.net> X-Original-From: Gregory Sandala Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Thu, 22 Mar 2007 09:26:58 +1100 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Gregory Sandala [sandala#,#chem.usyd.edu.au] Hi Julia, It looks like you're trying to run the program Gaussian for your CC jobs. In my experience, this is a very poor choice. The software package Molpro is far superior for these types of calculations and can run in parallel very efficiently. However, Molpro likes its memory; so, depending on your resources, this may limit you like the disk is limiting you in Gaussian. Best wishes, Greg On 22/03/2007, at 5:38 AM, Julia Subbotina ysubboti() ucalgary.ca wrote: > > Sent to CCL by: "Julia Subbotina" [ysubboti%a%ucalgary.ca] > Dear CCLers > I have a problem with running CCSD(T)\ Ahlrichs pVDZ single point > energy job. I am limited with my disc space (~110GB), but this job > seems to need even more (Transformation cannot fit in the specified > MaxDisk.). The input line is: > %mem=3GB > ccsd(t)/gen MaxDisk=100GB > And later I am expected to make a single point calculation for the > bigger system than one I am struggling with now. I need a > suggestion how i can handle this kind of problem. Any tips are > welcome. > > Thank you in advance, > Julia > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Wed Mar 21 22:16:00 2007 From: "Osman Guner oguner * turquoisecons.com" To: CCL Subject: CCL: CINF Scholarship for Scientific Excellence Sponsored by FIZ Chemie Berlin Message-Id: <-33869-070321143839-12345-DyQ+qUXx9iTi2ZRjplx9hw-$-server.ccl.net> X-Original-From: "Osman Guner" Date: Wed, 21 Mar 2007 11:22:56 -0700 Sent to CCL by: "Osman Guner" [oguner^turquoisecons.com] This is a reminder that the deadline for applying for the CINF-FIZ Scholarship for Scientific Excellence is approaching fast - April 2nd , 2007 CINF Scholarship for Scientific Excellence Sponsored by FIZ Chemie Berlin The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by FIZ Chemie Berlin is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Three scholarships valued at $1,000 each will be given out at the 234th ACS National Meeting in Boston, August 19 -23, 2007. Applicants have to be enrolled at a certified college or university. They have to present a poster during the Sci-Mix session at the National Meeting. Abstracts for the posters have to be submitted electronically through OASYS before April 2, 2007. Please, go to http://oasys.acs.org/acs/234nm/cinf/papers/index.cgi and click on Sci-Mix. To enter your abstract, just follow the instructions. At the same time, inform the Chair of the selection committee, Guenter Grethe at ggrethe#%#comcast.net, that you are applying for a scholarship. Additionally, a 2,000-word long abstract describing the work to be presented has to be sent in electronic form to the Chair of the selection committee by June 15, 2007. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced at the meeting. The contents shall reflect upon the student's work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked "Winner of the CINF-FIZ Chemie Berlin Academic Scientific Excellence" at the poster session. Guenter Grethe Dr. Guenter Grethe 352 Channing Way Alameda, CA 94502-7409 Tel/Fax: 510-865-5152 Mobile: 510-333-7526 e-mail: ggrethe#%#comcast.net Osman F. Guner, Ph.D Principal, Turquoise Consulting Web: http://www.turquoisecons.com/ Email: Oguner#%#turquoisecons.com Skype: turquoisecons From owner-chemistry@ccl.net Wed Mar 21 22:53:00 2007 From: "neeraj misra misraneeraj]^[gmail.com" To: CCL Subject: CCL: vibrational spectra Message-Id: <-33870-070321225141-15103-sv9uuLmQtSBes8RvkxI0MA]|[server.ccl.net> X-Original-From: "neeraj misra" Date: Wed, 21 Mar 2007 22:51:38 -0400 Sent to CCL by: "neeraj misra" [misraneeraj%x%gmail.com] I have been trying to calculate the vibrational spectra of a 90 atom molecule by semi empirical PM3 but no success so far .The structure gets optimized but fails to run for the frequency calculations.Please can anyone help me in this.I am attaching the input file of the molecule. 90 Sb 1.05300 7.25300 1.82800 O 0.35200 5.48400 0.83900 O -0.53400 6.88100 -0.65400 O -1.16600 4.93500 -2.33900 O 1.62800 8.87000 3.04200 O 0.86700 10.24900 1.46600 O 1.98300 12.35200 2.77000 C 2.35700 7.63000 0.22500 C 2.01900 8.43400 -0.85500 C 2.87200 8.48700 -1.94300 C 4.05000 7.76000 -1.94500 C 4.38200 6.98100 -0.85900 C 3.53400 6.90200 0.22100 C -0.96200 7.60000 2.34700 C -1.83900 8.33600 1.56800 C -3.17800 8.34700 1.91000 C -3.63500 7.65500 3.01700 C -2.74900 6.96600 3.81800 C -1.41200 6.93300 3.48700 C 2.10200 5.99100 3.15400 C 2.23800 4.63600 2.85400 C 3.05600 3.83600 3.63500 C 3.73600 4.35700 4.70400 C 3.60200 5.69600 5.00500 C 2.78800 6.51600 4.24200 C -0.32200 5.74500 -0.24100 C -0.88900 4.52700 -0.99200 C 0.20300 3.45600 -1.06300 C 0.16300 2.32000 -0.27100 C 1.21800 1.40200 -0.32800 C 2.28700 1.61900 -1.14700 C 2.33700 2.75900 -1.91700 C 1.29500 3.66700 -1.87600 C -2.18600 4.06900 -0.33400 C -2.94000 3.09700 -0.99400 C -4.18800 2.73100 -0.51900 C -4.69600 3.32800 0.61900 C -3.95100 4.25300 1.29800 C -2.71100 4.62900 0.81900 C 1.33400 10.05700 2.57400 C 1.57600 11.23200 3.55200 C 2.71200 10.91700 4.51300 C 3.95100 10.54700 3.98200 C 5.00400 10.22200 4.81400 C 4.84000 10.25700 6.18800 C 3.63000 10.63500 6.72600 C 2.57000 10.97100 5.89000 C 0.25800 11.49900 4.28600 C -0.47700 10.45400 4.82400 C -1.62300 10.70100 5.56000 C -2.05600 11.99200 5.75400 C -1.33700 13.03800 5.22400 C -0.18200 12.79700 4.49300 H -1.70400 5.55500 -2.33300 H 1.38800 12.54600 2.24000 H 1.23200 8.93000 -0.84700 H 2.65400 9.01300 -2.67900 H 4.61800 7.79900 -2.68000 H 5.18300 6.50700 -0.85600 H 3.75100 6.36100 0.94500 H -1.53400 8.81300 0.83000 H -3.78000 8.82800 1.38800 H -4.54300 7.65400 3.22100 H -3.05300 6.52600 4.57800 H -0.81000 6.46700 4.02200 H 1.78000 4.26900 2.13200 H 3.14400 2.93200 3.43100 H 4.28500 3.81400 5.22200 H 4.06300 6.05200 5.72900 H 2.70100 7.41600 4.45800 H -0.56100 2.16900 0.29500 H 1.19000 0.63700 0.19800 H 2.98000 1.00000 -1.18500 H 3.07000 2.91800 -2.46700 H 1.33100 4.43200 -2.40400 H -2.60000 2.69200 -1.75900 H -4.68300 2.08300 -0.96700 H -5.54500 3.10000 0.92300 H -4.28000 4.62800 2.08300 H -2.21900 5.27100 1.28000 H 4.06700 10.51900 3.05900 H 5.82400 9.97900 4.45000 H 5.54700 10.02500 6.74600 H 3.52200 10.66600 7.65000 H 1.75900 11.23600 6.25800 H -0.19800 9.57900 4.68900 H -2.10100 9.99300 5.92300 H -2.83100 12.15600 6.24000 H -1.62700 13.91300 5.35700 H 0.29900 13.51100 4.14100