From owner-chemistry@ccl.net Mon Dec 11 06:42:49 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA19709; Mon, 11 Dec 1995 06:33:21 -0500 Received: from rulway.leidenuniv.nl for frits@chemde4.leidenuniv.nl by bedrock.ccl.net (8.7.1/950822.1) id GAA16814; Mon, 11 Dec 1995 06:33:17 -0500 (EST) Received: from chemde4.LeidenUniv.nl by rulway.leidenuniv.nl with SMTP id AA26345 (5.67b/IDA-1.5 for <@RULWAY.LEIDENUNIV.NL:chemistry@ccl.net>); Mon, 11 Dec 1995 12:33:15 +0100 Received: by chemde4.leidenuniv.nl (920330.SGI/920502.SGI) for @RULWAY.LEIDENUNIV.NL:elewars@alchemy.chem.utoronto.ca id AA16614; Mon, 11 Dec 95 12:38:20 +0100 Date: Mon, 11 Dec 95 12:38:20 +0100 From: frits@chemde4.leidenuniv.nl (Frits Daalmans) Message-Id: <9512111138.AA16614@chemde4.leidenuniv.nl> To: "E. Lewars" Subject: Re: CCL:MATRIX ALGEBRA PROGRAM Cc: chemistry@ccl.net There are probably umpteen packages that can do that... what you could do is, grab a numerical library (say, lapack), and make a couple of wrapper functions (input of a matrix, output to screen/file, etc.) and make a "toolkit" of programs that use these routines. That's what I did (including the library itself :-( reinventing the wheel) but I am NOT sorry, because it is very convenient to be able to work with matrices just from the UNIX shell (with these tools) instead of writing programs for each case: i.e. (imaginary UNIX session) do some calculations, obtain some numerical results, use a tiny self-written tool to extract data from e.g. GAMESS or G94 output, mat_mult > C mat_eigval > Ceigval look at the eigenvalues, continue work,... If you are smart, you don't go this way but compile well-known freeware toolkits (I don't know of any though... if there are *really* *none* available I'll put mine under GPL and "publish" 'em). Good luck, Frits Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@chemde4.leidenuniv.nl Tel: [+31] (0)71-5274505 From tamasgunda@tigris.klte.hu Mon Dec 11 06:57:50 1995 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.6.10/950822.1) id GAA19792; Mon, 11 Dec 1995 06:44:58 -0500 Message-Id: <199512111144.GAA19792@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Mon, 11 Dec 1995 09:28:06 EST Sender: X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Mon, 11 Dec 1995 09:28:07 +1 Subject: Sybyl aromatic bonds Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Dear Netters, > > Have you ever used SYBYL? During the last few days, I was astonished to > find SYBYL does have problem in reading PDB files. Let me elaborate now. > [troubles with aromatic atoms deleted] The converison program Mol2mol can handle such a problems, as it uses a quite sophisticated algorithm to perceive the chemical surrounding of atoms, when reassigning of atom and bond types is necessary. Moreover, when converting to SYBYL or similar molecule file formats with extended atom types, the user can interfere and choose whether aromatic or single/double bond and atom types should be used in the output file. The program is available from Cherwell Scientific Publ., http://cherwell.com/cherwell, or info@cherwell.com Tamas E. Gunda ************************************************************************ Tamas E. Gunda, Ph.D. phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************