From mattacf@mcmail.CIS.McMaster.CA Sat Apr 11 01:23:49 1998 Received: from mcmail.CIS.McMaster.CA for mattacf@mcmail.CIS.McMaster.CA by www.ccl.net (8.8.3/950822.1) id AAA06315; Sat, 11 Apr 1998 00:52:19 -0400 (EDT) Received: from localhost (mattacf@localhost) by mcmail.CIS.McMaster.CA (8.8.5/8.8.5) with SMTP id AAA09759 for ; Sat, 11 Apr 1998 00:52:17 -0400 (EDT) Date: Sat, 11 Apr 1998 00:52:17 -0400 (EDT) From: "C.F. Matta" To: CCL Subject: Re: Protein Spreadsheet Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, For all of you who expressed interest in the LOTUS123 spreadsheet program (Peptides Geometry Calculations Spreadsheet PGCS01), the spreadsheet as well as a draft manual can be downloaded free of charge at the CCL archives: ftp://www.ccl.net/pub/chemistry/data/Protein-spreadsheet The respective names/sizes of the files to do download are: pgcs01.wk4 962 KB PGCS_manual.dot 1.1 MB (Note that the manual is an incomplete, rough first draft, as it is still in preparation. It will be announced when completed). SUMMARY OF PROGRAM CAPABILITIES: PGCS could handle polypeptides of as many as 8100 atoms. The input is the coordinates in PDB format. The program then computes backbone bond angles, distances and ALL sorts of backbone dihedrals that you may require (not only the usual phi, psi, and omega). In addition to a properly labeled list of dihedral, you also get the number of residues per turn, the height in A of each turn, the delta (twist) angle (twist between each residue as you look along the axis of the polypeptide, the N and t parameters. In addition, if you input the helix type (e.g. 3-10 helix, pi-helix, etc.) it will provide you with a properly labeled list of hydrogen bond distances and angles along the backbone. (In this way you can "test" an unknown peptide to find its type). The program can also compute the full distance matrix for peptides that are smaller than 250 atoms (but can be modified for larger ones up to 8100). After each calculation, it will automatically provide you with a labeled Ramachandran plot as well as averages of all the computed parameters. All what you need is to input the pdb info and familiarize yourself with the package. For the latter purpose, it comes with some test data. System requirement: any PC with any version of LOTUS123 Version 4 (or later) running under Windows. (This program is totally free of charge. I take no responsibility for any outcome of its use). I would appreciate any improvements/modifications suggestions or comments. Cheers. Cherif Matta Chemistry Department McMaster University 1280 Main St. W., Hamilton, Ontario Canada, L8S 4M1 email: mattacf@mcmail.cis.mcmaster.ca Phone: (905)-525-9140 - ext. 22502 Fax: (905)-522-2509 From qiang@tammy.harvard.edu Sat Apr 11 19:23:58 1998 Received: from tammy.harvard.edu for qiang@tammy.harvard.edu by www.ccl.net (8.8.3/950822.1) id SAA08647; Sat, 11 Apr 1998 18:36:40 -0400 (EDT) Received: from topanga.harvard.edu (topanga [128.103.92.179]) by tammy.harvard.edu (8.8.2/8.8.2) with ESMTP id SAA03990 for ; Sat, 11 Apr 1998 18:44:58 -0400 (EDT) Received: from localhost (qiang@localhost) by topanga.harvard.edu (8.8.2/8.8.2) with SMTP id SAA10501 for ; Sat, 11 Apr 1998 18:32:58 -0400 (EDT) Date: Sat, 11 Apr 1998 18:32:58 -0400 (EDT) From: Qiang Cui To: chemistry@www.ccl.net Subject: Local correlations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, folks. Just wonder if any one knows any popular packages that can handle local correlation methods at the MP2 or CCSD levels other than Molpro96? Thanks! ___________________________________________________________________________ Qiang Cui Dept. of Chem. _ __..-;''`--/'/ /.',-`-. Harvard Univ. (`/' ` | \ \ \\ / / / / .-'/`,_ 12 Oxford St., /'`\ \ | \ | \| // // / -.,/_,'-, Cambridge, MA 02138 /<7' ; \ \ | ; ||/ /| | \/ |`-/,/-.,_,/') (617)-495-8997 / _.-, `,-\,__| _-| / \ \/|_/ | '-/.;.\' (617)-495-1775 `-` f/ ; / __/ \__ `/ |__/ | `-' | -| =|\_ \ |-' | http://euch4m.chem.emory.edu/~qiang __/ /_..-' ` ),' // ((__.-'((___..-'' \__.' 65 Dane Street Somerville, MA 02143 (617)-623-5123 __________________________________________________________________________