From chemistry-request@server.ccl.net Wed Jul 18 19:06:40 2001 Received: from ozone.umsl.edu ([134.124.105.185]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6IN6e511931 for ; Wed, 18 Jul 2001 19:06:40 -0400 Received: from ozone.umsl.edu (localhost [127.0.0.1]) by ozone.umsl.edu (SGI-8.9.3/8.9.3) with ESMTP id SAA74157 for ; Wed, 18 Jul 2001 18:09:40 -0700 (PDT) Sender: siva@ozone.umsl.edu Message-ID: <3B563354.7F686867@ozone.umsl.edu> Date: Wed, 18 Jul 2001 18:09:40 -0700 From: Sivanesan Dakshanamurthy Organization: University of Missouri-St. Louis X-Mailer: Mozilla 4.51 [en] (X11; I; IRIX64 6.5 IP27) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: help Content-Type: multipart/alternative; boundary="------------94C67786569D363BAE72A179" --------------94C67786569D363BAE72A179 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I did linear correlation graph Expt. vs calculated B.E. for Enzyme-Substrate interactions. But I do need to compute (from my correlation plot) values of r**2, cross-validated r**2 (sometimes called q**2), F value, p value, etc., which would reveal the statistical quality of my linear regression. I would appreciate any suggessions about how to generate these various statistical parameters. Thanks in advance, Sincerely, D.Sivanesan -- ( @ @ ) -------------------------------------------o00o----(_)----o00o------------------ D. Sivanesan,Ph.D. | Post Doctoral Associate Fellow, |"SCIENCE IS NOT A FANCY WORD ITS A Department of chemistry | TOOL TO UNDERSTAND, UNUNDERSTANDABLE Computational Chemistry Group, | NATURE'S PHENOMENA" Centre for Molecular Electronics, | : : University of Missouri, | : : St. Louis, Missouri-63121. USA | : Phone: 314-516-6882 (Office) | : : | : : E-mail: siva@ozone.umsl.edu | : chedsiva@jinx.umsl.edu | : : Fax : 314-516-5342 | : : -------------------------------------------------------------------------------- --------------94C67786569D363BAE72A179 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers,

I did linear correlation graph Expt. vs calculated B.E. for Enzyme-Substrate interactions. But I do need to compute (from my correlation plot) values of r**2, cross-validated r**2 (sometimes called q**2), F value, p value, etc., which would reveal the statistical quality of my linear regression. I would appreciate any suggessions about how to generate these various statistical parameters.

Thanks in advance,
Sincerely,
D.Sivanesan

-- 
                                                 ( @ @ )
-------------------------------------------o00o----(_)----o00o------------------
D. Sivanesan,Ph.D.                    | 
Post Doctoral Associate Fellow,       |"SCIENCE IS NOT A FANCY WORD ITS A      
Department of chemistry               | TOOL TO UNDERSTAND, UNUNDERSTANDABLE
Computational Chemistry Group,        | NATURE'S PHENOMENA"
Centre for Molecular Electronics,     |           :     :
University of Missouri,               |            :   :
St. Louis, Missouri-63121. USA        |              : 
Phone: 314-516-6882 (Office)          |            :   :
                                      |           :   :
E-mail: siva@ozone.umsl.edu           |             :  
        chedsiva@jinx.umsl.edu        |            :  :  
Fax : 314-516-5342                    |           :    :  
--------------------------------------------------------------------------------

--------------94C67786569D363BAE72A179-- From chemistry-request@server.ccl.net Thu Jul 19 06:03:12 2001 Received: from mailweb17.rediffmail.com (IDENT:qmailr@[203.199.83.141]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6JA39531970 for ; Thu, 19 Jul 2001 06:03:10 -0400 Received: (qmail 27721 invoked by uid 510); 19 Jul 2001 10:05:03 -0000 Date: 19 Jul 2001 10:05:03 -0000 Message-ID: <20010719100503.27720.qmail@mailweb17.rediffmail.com> Received: from unknown (203.145.139.252) by rediffmail.com via HTTP; 19 Jul 2001 10:05:03 -0000 MIME-Version: 1.0 To: "CHEMISTRY@CCL.NET" Subject: CONTOUR DIAGRAMES From: "RAJNISH MOUDGIL" Content-ID: Content-type: text/plain Content-Description: Body Content-Transfer-Encoding: 7bit Dear CCl i am a Ph.D student working on the theoretical studies on Se and Si compounds. I want to draw molecular orbital contour diagrames using coefficients from Gaussian and games outputs, I would greatly appreciate if any body could tell me how to draw these diagrames. Is there special kind of software, If so, then how to get, from where to get. is it commercial or non commercil or is it avialable somwhere in the internet free of cost.Any reply would be gretly acknowledged. Sincerely Rajnish Moudgil Department of Chemistry Guru Nanak Dev University Amritsar-143005 India ____________________________________________________ http://www.monsterindia.com - The Best Jobs. For the Best Minds. From chemistry-request@server.ccl.net Wed Jul 18 15:12:34 2001 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6IJCY501868 for ; Wed, 18 Jul 2001 15:12:34 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Subject: Announcing PyMOL v0.56 (+ Windows Installer) X-MIMEOLE: Produced By Microsoft Exchange V6.0.4417.0 Date: Wed, 18 Jul 2001 12:11:49 -0700 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Announcing PyMOL v0.56 (+ Windows Installer) Thread-Index: AcEPvX8cNuZg8ZahT+SUMMC2PfsS9Q== From: "DeLano, Warren" To: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id f6IJCY501869 PyMOL v0.56 has been released http://pymol.sourceforge.net . An illustrated manual is available on the web page, and the program is now considered late beta-test quality. PyMOL is a full-featured molecular graphics and animation program, and will eventually support building and molecular modeling. PyMOL lays the groundwork for a completely free and open-source replacement for packages such as Grasp, Molscript/Raster3D, O, Midas, Insight II, Cerius2, Sybyl, and Quanta. Why pay MSI or Tripos for expensive tools if you can accomplish the same task with free software? Plus, you can deploy PyMOL on every machine in your lab or company for no cost other than hardware (approx. $100/PC for an nVidia Gefore2/MX video card). PyMOL has most of the visualization features you would expect for maps and molecules, with the exception of cartoon ribbons, which require Molscript for generation of the 3D geometries as Raster3D input files. I am still looking for donation of unrestricted source-code for a high-quality ribbon-rendering algorithm (any volunteers?). PyMOL is an optimal solution for generating PowerPoint figures on your Windows desktop (PNG files directly import into PowerPoint) and can also be used for live 3D molecular graphics on an LCD projector if you have a Dell or Toshiba laptop that contains an nVidia GeForceGo chip. I have confirmed that a DELL Inspiron 8000 will significantly outperform an SGI Octane/MXE for molecular graphics. Although there are other similar efforts underway (Birdwash, CCP4-3d, MolKit, etc.), PyMOL is currently ahead of the other efforts in terms of visualization capabilities and accessibility to non-developers under Windows. Right now, PyMOL is the most powerful molecular graphics program based entirely on free and unrestricted source-code (No GPL!). Unlike RasMOL, PyMOL is targeted towards the needs of professionals, not undergraduates, and supports features such as robust molecular editing, animations, scripting, ray-tracing, and programmable extensibility. Python lovers will be happy to learn that PyMOL uses an embedded Python interpreter as its native API, and maps it to an expandable, hyper-efficient command language. Pure Python-based interfaces to programs such as Amber, CNS, CCP4, GAMESS, or your own projects can easily be developed as needs arise (for example, in graduate student projects!) A Windows installer can be found at: http://prdownloads.sourceforge.net/pymol/pymol-0_56-bin-win32-py152.zip and requires Python 152 http://prdownloads.sourceforge.net/pymol/py152.exe Source code for unix can be obtained and compiled through the publicly accessible CVS repository. Linux RPMs will be released by the end of the summer. Please see the web site for additional information: http://pymol.sourceforge.net http://www.pymol.org Enjoy! Warren -- mailto:warren@sunesis.com Warren L. DeLano, Ph.D. From chemistry-request@server.ccl.net Thu Jul 19 11:26:18 2001 Received: from garnet.INS.cwru.edu (root@[129.22.8.233]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6JFQI531784 for ; Thu, 19 Jul 2001 11:26:18 -0400 Received: from gavin (chem51286.CHEM.CWRU.Edu [129.22.129.217]) by garnet.INS.cwru.edu with SMTP (8.11.2+cwru/CWRU-3.8) id f6JFQIY06492; Thu, 19 Jul 2001 11:26:18 -0400 (EDT) (from hxt10@po.cwru.edu for ) Message-ID: <001201c11067$d550c200$d9811681@cwru.edu> Reply-To: "Hui-Hsu $Gavin$ Tsai" From: "Hui-Hsu $Gavin$ Tsai" To: Subject: negative vibration frequency Date: Thu, 19 Jul 2001 11:31:08 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000F_01C11046.4DFBFE80" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_000F_01C11046.4DFBFE80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi CCLers: I have a question about the negative frequency in the frequency = calculation. For larger or complicate molecule, the geometry optimization usually can = not reach the minimum point, but the saddle point with some negative and = small vibration frequencies. To adapt and try to reoptimize the molecule = wastes CPU. Is there any geometry optimization algorithm which can follow the = negative frequency and reach the minimum point automatically? any comment is welcome! Thanks! Gavin=20 ------=_NextPart_000_000F_01C11046.4DFBFE80 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi CCLers:

I have a question = about the=20 negative frequency in the frequency calculation.

For larger or complicate molecule,=20 the geometry optimization usually can not reach the minimum = point,=20 but the saddle point with some negative and small vibration=20 frequencies. To adapt and try to reoptimize the molecule wastes=20 CPU.

Is there any geometry optimization = algorithm which=20 can follow the negative frequency and reach the minimum point=20 automatically?

any comment is welcome! = Thanks!

Gavin

------=_NextPart_000_000F_01C11046.4DFBFE80-- From chemistry-request@server.ccl.net Thu Jul 19 08:00:23 2001 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6JC0N512990 for ; Thu, 19 Jul 2001 08:00:23 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id OAA06390 ; Thu, 19 Jul 2001 14:00:04 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id NAA06302; Thu, 19 Jul 2001 13:58:09 +0200 Date: Thu, 19 Jul 2001 13:58:09 +0200 Message-Id: <200107191158.NAA06302@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: vani@reef.phys.lsu.edu CC: chemistry@ccl.net In-reply-to: (message from Vemparala Satyavani on Wed, 18 Jul 2001 10:32:08 -0500 (CDT)) Subject: Re: CCL:atom names in PDB files References: > ATOM 1 N GLN A 1 63.870 -23.035 -4.001 1.00 2.09 > MCP1 N > ATOM 2 CA GLN A 1 65.000 -22.112 -3.695 1.00 1.89 > MCP1 C > ATOM 3 C GLN A 1 64.534 -20.647 -3.880 1.00 1.67 > MCP1 C > > my question is there are 2 Nitrogens, 5 carbons etc.,..in Glutamine > residue. how would i know which corresponds to what? Each atom has a unique name, for example, the "CA" is the alpha carbon, and "C" is the carbon in the peptide group. Check the PDB specification for details. However, some programs use their own naming rules instead of those defined by the PDB, including widespread codes such as CHARMM and XPlor. And for hydrogens, the chaos is almost perfect. Moreover, not all programs respect the rules for atom name justification (right justification for the element symbol, left justification for the unique identification part). Alpha-carbons thus are frequently labelled as calcium atoms. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jul 19 13:38:43 2001 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6JHch502166 for ; Thu, 19 Jul 2001 13:38:43 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id NAA08570; Thu, 19 Jul 2001 13:29:19 -0400 (EDT) Date: Thu, 19 Jul 2001 13:29:19 -0400 From: Rick Venable To: Konrad Hinsen cc: vani@reef.phys.lsu.edu, chemistry@ccl.net Subject: Re: CCL:atom names in PDB files In-Reply-To: <200107191158.NAA06302@chinon.cnrs-orleans.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 19 Jul 2001, Konrad Hinsen wrote: > > ATOM 1 N GLN A 1 63.870 -23.035 -4.001 1.00 2.09 > > MCP1 N > > ATOM 2 CA GLN A 1 65.000 -22.112 -3.695 1.00 1.89 > > MCP1 C > > ATOM 3 C GLN A 1 64.534 -20.647 -3.880 1.00 1.67 > > MCP1 C > > > > my question is there are 2 Nitrogens, 5 carbons etc.,..in Glutamine > > residue. how would i know which corresponds to what? > > Each atom has a unique name, for example, the "CA" is the alpha > carbon, and "C" is the carbon in the peptide group. Check the PDB > specification for details. > > However, some programs use their own naming rules instead of those > defined by the PDB, including widespread codes such as CHARMM and > XPlor. And for hydrogens, the chaos is almost perfect. Moreover, not > all programs respect the rules for atom name justification (right > justification for the element symbol, left justification for the > unique identification part). Alpha-carbons thus are frequently > labelled as calcium atoms. CHARMM follows the same alpha-amino acid atom name conventions as PDB wrt. heavy atoms for the most part; the exceptions are few (C terminal O atoms, CD vs. CD1 for ILE). The only other major issue for CHARMM is for the HIS residue; CHARMM has 3 separate residues (HSD, HSE, HSC) depending on the protonation state. PDB2 format includes the element symbol, so that CA should be recognized as a carbon atom, if the newer format is used. Hydrogen naming is systematic in most cases, just different; it's so difficult to deal with the 1:1 correspondence of H atom names that it's usually not worth the effort. If you want to see real chaos, try looking at the heavy atom labels that come from data extracted from the Cambridge small molecule database, e.g. for saccharides. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 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 Thu Jul 19 13:21:12 2001 Received: from prserv.net ([32.97.166.34]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6JHLC501998 for ; Thu, 19 Jul 2001 13:21:12 -0400 Received: from attglobal.net (slip-12-64-6-147.mis.prserv.net[12.64.6.147]) by prserv.net (out4) with SMTP id <2001071917211120404uoar7e>; Thu, 19 Jul 2001 17:21:11 +0000 Message-ID: <3B56C3E4.5FEBB1FB@attglobal.net> Date: Thu, 19 Jul 2001 12:26:28 +0100 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.51 [en]C-CCK-MCD (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Torsion angles Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, A possible challenge of the day ... Getting correct [acyclic, of course] torsion angles in conjugated systems... If I have missed the general solution to this quandry please forgive the band width, and let me know. There have been many methodologies put forth for computing [gas phase] molecular geometries. Some are expensive, and some are quite inexpensive. They all have parameters [To CI or not To CI, basis set, USS,UPP, Beta, exponents, etc.] Some get bond lengths and bond angles correct. At nearly all levels of theory it seems difficult to get torsion angles dependably at an acceptable, approximate, affordable cost. B3LYP can be an acceptable fall back when all the semiempirical methods fail, and they seem to in my experience over >25 years at doing chromophore design.. But B3LYP usually gets things too flat, i.e.Ph-N=N-Ph, and when there is the possibility of internal hydrogen bonding, even between SP2 N and SP2 or Sp3 O, and a H attached to an aromatic ring. MP2 is only slightly better. Some of the best results I have seen were done > 25 years ago when Birner [Leipzig, I think] simply added to lowly INDO all the 2-center computed over Slater functions..... Yes there has been a lot of progress, but I still see opportunities. Comments? John McKelvey From chemistry-request@server.ccl.net Thu Jul 19 15:32:58 2001 Received: from physics.lsu.edu ([130.39.182.96]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6JJWw504728 for ; Thu, 19 Jul 2001 15:32:58 -0400 Received: from localhost (vani@localhost) by physics.lsu.edu (8.9.2/8.9.2) with ESMTP id OAA19833 for ; Thu, 19 Jul 2001 14:32:16 -0500 (CDT) Date: Thu, 19 Jul 2001 14:32:16 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: identifying box size for a PDB file Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, thankyou for answering the previous query. Iam trying to do Molecular dynamics simulation of some protein. I can get the starting structure from the PDB file (the cartesian coordinates). But how can i find the box size for that structure for MD? thanks vani