From owner-chemistry@ccl.net Thu Apr 27 00:27:01 2006 From: "Yao-Ying Chien chieny[]msu.edu" To: CCL Subject: CCL: intramolecular interaction energy Message-Id: <-31605-060426235109-12010-5XbS3XDiYTqxKukhpZvAbw/./server.ccl.net> X-Original-From: Yao-Ying Chien Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=Big5 Date: Wed, 26 Apr 2006 22:05:53 -0400 MIME-Version: 1.0 Sent to CCL by: Yao-Ying Chien [chieny~~msu.edu] Hi, I am interested in "interaction energy" both inter- and intramolecular. Any good review articles or just papers to help me start are appreciated. Many thanks, Yao-Ying Chien Michigan, USA Jozsef Csontos jozsefcsontos**creighton.edu said the following on 2006/4/24 ¤U¤È 04:02: >Sent to CCL by: Jozsef Csontos [jozsefcsontos,,creighton.edu] >Dear List Members, > >I'm interested in calculating intramolecular interactions in proteins. > >When the interacting groups are far from each other considering the >primary structure/sequence, I usually do the following: > >1, cut somewhere (close to the groups) the structure; remove the "extra >stuff"; put some auxiliary atoms/groups on the free valences. >2, calculate the BSSE corrected interaction energy > >The above procedure, which is based on the separated interacting systems >situation is accepted or at least widely used in the literature:) > >My problem is, what if the interacting groups are close to (or next to) >each other on the sequence, too? I shouldn't cut bonds, because it's >like to cutting the C2-C3 bond in the gauche-butane to calculate the C1, >C4 interaction and I'd be in trouble to complete the valences, because >of the close proximity of the auxiliary atoms. > >I've some idea to use the non-folded conformation as the reference >system and its basis functions to calculate the BSSE, however, I'd be >pleased if you give me some ideas/references or just correct me. > > >Cheers, >Jozsef > > > -- Yao-Ying Chien 517-402-8808 911 W. Cavanaugh Rd., Apt #10, Lansing, MI 48910 From owner-chemistry@ccl.net Thu Apr 27 06:24:00 2006 From: "Nuno Loureiro Ferreira nunolf(0)ci.uc.pt" To: CCL Subject: CCL: Salt bridges - proteins Message-Id: <-31606-060427061932-22758-gsdV3XHebrPatZRHza6LGw]![server.ccl.net> X-Original-From: "Nuno Loureiro Ferreira" Date: Thu, 27 Apr 2006 06:19:29 -0400 Sent to CCL by: "Nuno Loureiro Ferreira" [nunolf.|*|.ci.uc.pt] Hi CCLers Is there a program/script running on unix/linux to determine salt-bridges on protein structures? > From what I read, we can infer if there's a salt bridge for a pair of oppositely charged residues if: - the centroids of the side-chain charged groups in oppositely charged residues lie within 4.0 angstrons of each other [Barlow & Thornton, 1983] and - at least one pair of Asp or Glu side-chain carboxyl oxygen atoms and side-chain nitrogen atoms of Arg, Lys or His are within a 4.0 ang. distance [Kumar & Nussinov, 1999] If there's out there an implementation doing something similar, I would appreciate to be informed. Best regards, Nuno From owner-chemistry@ccl.net Thu Apr 27 08:53:00 2006 From: "Niklas Loges Niklas.Loges()web.de" To: CCL Subject: CCL: CaCO3-force field calculations Message-Id: <-31607-060427071944-15873-iHRlm8x0u78wybGFCIJNlA[#]server.ccl.net> X-Original-From: "Niklas Loges" Date: Thu, 27 Apr 2006 07:19:44 -0400 Sent to CCL by: "Niklas Loges" [Niklas.Loges*web.de] Hi, I want to use force field molecular dynamics calculations to investigate the interactions of some calcite (CaCO3) surfaces with organic molecules. I've found some papers about (N.H. deLeeuw; S. Parker), they have used the cvff with additional parameters for Ca2+ and the carbonate-ions. My question is how to add these parameters [published in Phys. Chem. Minerals 23 (1996), 89-93] to the existing cvff force field? Can anyone help me? Thanks a lot! Niklas Loges University of Mainz, Germany From owner-chemistry@ccl.net Thu Apr 27 09:28:00 2006 From: "Anderson Coser Gaudio anderson:+:npd.ufes.br" To: CCL Subject: CCL: MoCalc: Molecular Calculation Interface. Version 2.2. Message-Id: <-31608-060427081555-25676-22G/Rq5f0xbq5PJ/13cigw{}server.ccl.net> X-Original-From: "Anderson Coser Gaudio" Date: Thu, 27 Apr 2006 08:15:54 -0400 Sent to CCL by: "Anderson Coser Gaudio" [anderson(_)npd.ufes.br] Dear colleagues, It is a pleasure to announce the release of MoCalc 2.2 software. MoCalc: Molecular Calculation Interface is a graphical user interface for the molecular calculation programs Gamess, Mopac, Tinker. MoCalc helps the user in the preparation of input files, the submission of calculations, the analysis of the results and the visualization of the involved chemical structures. Some properties can also be calculated by MoCalc. See details in reference: Depizzol, D.B.; Paiva, M.H.M.; Dos Santos, T.O.; Gaudio, A. C.; MoCalc: A New Graphical User Interface for Molecular Calculations J. Comput. Chem, 26(2), 142-144, 2005. The main features of MoCalc 2.2 are: (1)Create and handle Gamess, Mopac, and Tinker input files; (2)Fast conversion of Gamess, Mopac, and Tinker input and output files, through the Babel program. The conversion may involve several files in just one procedure; (3)Fast conversion of external files of the types Gamess output, Mopac input, Mopac output, Tinker input, Hyperchem, Protein Data Bank, Sybyl, and Spartan; (4)Import multiple external files of types Gamess output, Mopac input, Mopac output, Tinker input, Hyperchem, Protein Data Bank, Sybyl, and Spartan to MoCalc system, converting them from their original format into Gamess input, Mopac input, or Tinker input document; (5)Edit and validate the keywords CONTRL, SYSTEM, BASIS,DRC, FORCE, MOROKM, MP2, PCM, SCF and STATPT that control the Gamess calculation procedure; (6)Edit and validate all keywords that control the Mopac calculation procedure; (7)Display the input (Mopac and Tinker) and output (Gamess, Mopac, and Tinker) molecular geometries through the RasMol program; (8)Run single or multiple (batch) calculations, either interactively or in background, and automatically open the output files as soon as the calculation finishes; (9)Energy minimization and global minimum energy search can be proceed through molecular mechanics (MM3) methodology (Tinker); (10)Calculation of molecular surface area and volume, and vibrational analysis (Tinker); (11)Extract results from the output files, such as energy, charges, dipole, interatomic distances, population analysis, wave function, bond orders, and valence analysis, and display them in spreadsheets; (12)Calculate reactivity indices derived from the frontier orbital theory and the root mean square (RMS) deviation of input and output geometries; (13)All results generated by MoCalc can be immediately transferred to text editors and spreadsheets; (14)The calculation results can be exported to HTML files; (15)When more than one Gamess/Mopac output files are opened, MoCalc can run a comparative analysis of the results in those files by showing the values of many properties in a spreadsheet. MoCalc also generate a graphical comparison of these properties; (16)Graphical interface with menu and pop up menu system, toolbar, status bar, pathname bar, and file tree display; (17)The pop up menu system allows the user to run calculation and handles ()Gamess, Mopac, and Tinker documents; (18)MoCalc is available only in English; (19)Complete English help file in PDF format; (20)Gamess, Mopac, Tinker, Rasmol, and Babel manuals also available. MoCalc 2.2 can be freely downloaded from its official web site, which can be accessed through the authors homepage (see below). Please, test it, use it, enjoy it, and cite it. Send suggestions to the authors e-mail below. Dr. Anderson Coser Gaudio Physics Department Federal University of Esprito Santo 514, Fernando Ferrari Av. - Goiabeiras 29075-910 Vitria-ES Tel. +55-27-3335.2483 Fax. +55-27-3335.2823 http://www.cce.ufes.br/anderson anderson~~npd.ufes.br Skype: acgaudio From owner-chemistry@ccl.net Thu Apr 27 11:03:00 2006 From: "Jozsef Csontos jozsefcsontos_-_creighton.edu" To: CCL Subject: CCL: Software for melting point analysis of DNA duplex Message-Id: <-31609-060427110118-24855-1ReyKP1JgkHXeavq04YZ0w|-|server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 27 Apr 2006 10:01:08 -0500 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos###creighton.edu] Hi, usually, DNA melting-point calculation is based on the primary sequences of the fragments. So, I don't think there exists out there such a specific software you want. (anyway, you can do some MD calculations on your structures) Cheers, Jozsef On Wed, 2006-04-26 at 23:32 -0400, Raji Raji raji*anal.chem.tohoku.ac.jp wrote: > Sent to CCL by: "Raji Raji" [raji%a%anal.chem.tohoku.ac.jp] > > Dear CCL members, > Can any one tell me a best and freely available (academic purpose)software which can calculate the melting point of DNA duplex alone/DNA duplex with drug molecule/DNA duplex with some common lession like AP site(s). Also, it must allow me to load the .pdb/.mol2/.xyz files of the DNA duplex and drug molecule. MeltDNA (from Abhishek Tiwari et al.)works well for simple DNA duplex with and without mismatch. But it seems, this software doesn't provide an option to upload the DNA duplex files and no way to include drugs and AP site(s). > Thank you very much in advance. > Best Regards, > Raji.> > > -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Thu Apr 27 11:37:01 2006 From: "James Justin Robinson james.robinson]~[evotec.com" To: CCL Subject: CCL:G: Gaussian problems; Melanie Trusselle query Message-Id: <-31610-060427111211-436-02uYUYMEdxl9IV8LaaCfyw:server.ccl.net> X-Original-From: "James Justin Robinson" Date: Thu, 27 Apr 2006 11:12:07 -0400 Sent to CCL by: "James Justin Robinson" [james.robinson() evotec.com] Hi, You Gaussian input needs a blank line between title and charge/multipilicity. Also add a few blank lines after the input of the second z-matrix, this does help sometimes. If you have Molden, check that the atom ordering are the same and if problems persist I suggest you try a saddle calculation using MOPAC and use cartesian coordinates for the two input structures in your mopac saddle calculation. I cannot immediately recall how the out from NMR jobs compare to TMS. Some calculation often need to be compared to TMS to compare calculations, you may need the difference between TMS and your calculated molecule. I also suspect that the basis set for your NMR calculation maybe too small, daft I know, but perhaps 6-311+(2d,p) may be more adequate. Also I think the NOSYMM keyword is useful Hope this helps or at least causes some thought. Dr James J Robinson Evotec, Oxford. From owner-chemistry@ccl.net Thu Apr 27 15:27:00 2006 From: "Jan Jensen jan-jensen.*.uiowa.edu" To: CCL Subject: CCL: Ghemical-GMS/GTK-GAMESS version 2.00 Message-Id: <-31611-060427145358-24156-uIdCwhjue3SaaKUi8ai+qw*server.ccl.net> X-Original-From: "Jan Jensen" Date: Thu, 27 Apr 2006 14:53:58 -0400 Sent to CCL by: "Jan Jensen" [jan-jensen-x-uiowa.edu] Hi, The GAMESS GUI and queuing program Ghemical-GMS/GTK-GAMESS version 2.00 is now available and can be downloaded from http://www.uiowa.edu/~ghemical There are several new features including the ability to select and freeze atomic positions and bond lengths during energy minimizations (including the generation of appropriate keywords in the GAMESS input file). The installation procedure has also been simplified considerably, especially for MacOS X Best regards, Jan Jensen From owner-chemistry@ccl.net Thu Apr 27 17:49:01 2006 From: "Wayne Steinmetz WES04747{}pomona.edu" To: CCL Subject: CCL: Software for melting point analysis of DNA duplex Message-Id: <-31612-060427174716-27247-8+4vcRJZBkwaSgsIpMiJ2Q-.-server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 27 Apr 2006 14:46:13 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747/a\pomona.edu] I doubt that one can calculate accurately via modeling the quantities for the systems that you describe. First, getting the energy changes correct is very challenging. Second, the melting point is related to the Gibbs free energy. One requires a good value of both the enthalpy and the entropy change. Obtaining delta S is outside the limits of modeling software for the systems that you describe. George Whitesides > from Harvard made this point frequently and emphatically in his spring, 2006 Robbins Lectures at Pomona. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz#pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry#ccl.net [mailto:owner-chemistry#ccl.net] Sent: Wednesday, April 26, 2006 7:20 PM To: Wayne Steinmetz Subject: CCL: Software for melting point analysis of DNA duplex Sent to CCL by: "Raji Raji" [raji%a%anal.chem.tohoku.ac.jp] Dear CCL members, Can any one tell me a best and freely available (academic purpose)software which can calculate the melting point of DNA duplex alone/DNA duplex with drug molecule/DNA duplex with some common lession like AP site(s). Also, it must allow me to load the .pdb/.mol2/.xyz files of the DNA duplex and drug molecule. MeltDNA (from Abhishek Tiwari et al.)works well for simple DNA duplex with and without mismatch. But it seems, this software doesn't provide an option to upload the DNA duplex files and no way to include drugs and AP site(s). Thank you very much in advance. Best Regards, Raji.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. From owner-chemistry@ccl.net Thu Apr 27 20:10:00 2006 From: "Young Leh youngleh*_*gmail.com" To: CCL Subject: CCL: Basis Set for Transition Metals Message-Id: <-31613-060427200914-32449-J9pkSqFr45Mr7lNj4nZb3g%x%server.ccl.net> X-Original-From: "Young Leh" Date: Thu, 27 Apr 2006 20:09:13 -0400 Sent to CCL by: "Young Leh" [youngleh(_)gmail.com] Dear CCLer, I am unfortunately working on transition metals on which the standard basis sets give poor energies. Could somebody please recommend better basis sets that works for transition metals like Cu? From owner-chemistry@ccl.net Thu Apr 27 21:34:00 2006 From: "Jason D Acchioli jsd44{:}cornell.edu" To: CCL Subject: CCL: ONIOM and transition states Message-Id: <-31614-060427135312-18599-haKAV/2B9LYv4gwhJ92Rbw|*|server.ccl.net> X-Original-From: "Jason D'Acchioli" Content-Type: multipart/mixed; boundary="------------060300080300090301000707" Date: Thu, 27 Apr 2006 13:53:05 -0400 MIME-Version: 1.0 Sent to CCL by: "Jason D'Acchioli" [jsd44++cornell.edu] This is a multi-part message in MIME format. --------------060300080300090301000707 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi all, Does anyone have any experience with ONIOM? My main concern is with vibrational frequency calculations and transition states. Let's say, hypothetically speaking, that I want to do a calculation on a species containing a tBu group. It's been my experience that vibrational frequency analyses will give low energy (ca. 35 cm-1) imaginary frequencies corresponding to "methyl twitchings". If I do an ONIOM (or any type of QM/MM calculation, for that matter) calculation on the same system, will I observe the same type of imaginary frequencies? If I do, how drastically will this affect any transition state searches I do? Thanks, Jason -- *************************** Jason D'Acchioli, Ph.D. Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14850 Phone: 607-255-0597 e-mail: jsd44:-:cornell.edu *************************** --------------060300080300090301000707 Content-Type: text/x-vcard; charset=utf-8; name="jsd44.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="jsd44.vcf" begin:vcard fn:Jason D'Acchioli n:D'Acchioli;Jason org:Cornell University;Department of Chemistry and Chemical Biology adr:;;220C Baker Laboratory;Ithaca;NY;14853;USA email;internet:jsd44:-:cornell.edu title:Postdoctoral Research Associate tel;work:607-255-0597 tel;cell:614-404-5858 version:2.1 end:vcard --------------060300080300090301000707--