From Y0H8797@ACS.TAMU.EDU Sat May 18 17:53:47 1996 Received: from VMS1.TAMU.EDU for Y0H8797@ACS.TAMU.EDU by www.ccl.net (8.7.1/950822.1) id RAA24202; Sat, 18 May 1996 17:38:17 -0400 (EDT) Date: Sat, 18 May 1996 16:37:48 -0500 (CDT) From: YONG HUANG To: CHEMISTRY@www.ccl.net Message-Id: <960518163748.20c2c956@ACS.TAMU.EDU> Subject: Summary: Drawing program to generate Z-matrix I asked a question of any drawing program we can use to generate the Z-matrix. The following is a summary (plus my comments). Many thanks to everybody that helps me. ------Yong From: SMTP%"Y0H8797@ACS.TAMU.EDU" 7-MAY-1996 22:32:30.93 Subj: CCL:M:Drawing program to generate Z-matrix Does anybody know a drawing program we can use to generate the Z-matrix for DOS or Windows? I know CAChe Editor is very good but it's for Mac. (CAChe Editor combines with CAChe MOPAC can generate Z-matrix but Editor alone can't). It's better to be a freeware or shareware. Thank you for any response. Yong From: SMTP%"chpajt@bath.ac.uk" 8-MAY-1996 04:02:34.34 Subj: Re: CCL:M:Drawing program to generate Z-matrix Just a thought, cannot you use xmol of the pc to convert from carts to z-matrix? Alex [Comment: I need a drawing program I draw a molecule from scratch and the program generates the Z-matrix. Xmol is probably not what I want. Thanks, Alex.] From: SMTP%"gedeck@organik.uni-erlangen.de" 8-MAY-1996 08:07:47.70 Subj: Re: CCL:M:Drawing program to generate Z-matrix you might like to have a look at MolEdit which might do what you want. It combines a text editor with a molecular viewer, so it lets you control your current input file. It's not a click and draw program, because I prefer to write my Z-matrix by hand. MolEdit is available both as a DOS and a Windows version. The windows version is still beta, so not everything works but it's basic features are ok. Have a look at my home page http://www.organik.uni-erlangen.de/clark/gedeck/ Please drop me a note, if you download the windows version and especially if you have ideas about its improvement or bug reports. Yours sincerely, Peter Gedeck [Comment: Thanks, Dr. Gedeck. Again it's not what I want. But I tried it. It worked great as you said.] From: SMTP%"pherman@cache.com" 8-MAY-1996 11:19:45.85 Subj: Z-matrix [Comment: Dr. Peter Herman from CAChe e-mailed me about another question of mine (Given a Z-matrix, ask CAChe Editor to generate the molecule picture file.) Quite a few other programs can do this but it's not so obvious by CAChe Editor. Later Dr. Manli Zheng also answered this question. I'm not including it here but if you need it I'll e-mail you.] Peter From: SMTP%"manliz@cache.com" 8-MAY-1996 11:30:26.80 Subj: Re: CCL:M:Drawing program to generate Z-matrix Hi, Yong, The CAChe standalone PC will do this indirectly, in that if the user runs MOPAC, they will get a Z Matrix in the MOPAC Input file. However, there is no way to do this directly, since there is no user interface for MOPAC. On the Mac, you could select the molecule, and then do "Create MOPAC Input" from the Options menu, and have a Z Matrix in the MOPAC Input file generated. Manli Zheng, Ph.D. From: SMTP%"lwilson@LaSierra.EDU" 8-MAY-1996 19:44:03.06 Subj: Re: CCL:M:Drawing program to generate Z-matrix Dear Yong; PCMODEL from Serena Software is relatively inexpensive for academia and works very well. I use it to generate Z-matrices for MOPAC to operate on. CONVENIENT to draw and save files in different formats. Serena Software Box 3076 Bloomington, IN 47402-3076 812-333-0823 Hope this helps, lee wilson Chem. Dept. La Sierra University Riverside, CA 92515 From: SMTP%"jsb2@camsoft.com" 8-MAY-1996 20:41:31.00 Subj: Re: CCL:M:Drawing program to generate Z-matrix CS Chem3D can do this. Also, I'm pretty sure that CAChe is now available for Windows. More information about CS Chem3D is available from http://www.camsoft.com I'm not sure, but http://www.cache.com would be a good guess for info on CAChe Jonathan Brecher CambridgeSoft Corporation From: SMTP%"cmrag@mlucom.urz.Uni-Halle.DE" 10-MAY-1996 03:49:26.53 Subj: CCL:G:Z-matrix generation Yes. There is such a program for MS-Windows it is called StrukEd. Even the LITE-version can do all those things you are expecting: - 2D drawing with mouse and to assemble templates from menue - 2D >> 3D conversion (very reliable results with possible conformers in the cyclic substructures, you can chose those you want) - interactive modification of all degrees of struc tural freedom - automatic generation of Z-Matrix - interactive modification of Z-Matrix and constraints of optimisation - write MOPAC input files - read MOPAC output files - draws MOPAC structures, charges, orbitals etc. - supported data handling (internal database) - empirical calculation of atomic charges from topology (PEOE) - empirical calculation of molecular polarisability - Huckel-Molecular Orbitals from topology (visualisation of P-Matrix and orbitals) The full-Version can do additional things like: - handling up to 10 structures in separate Windows (for comparison) - RMS of similar structures (you can chose which pairs are taken into account) - generation of INPUT and reading OUTPUT for molecular mechanics and quantum mechanics standard programs (here not included) - PIMM, ZINDO, GAMESS, GAUSSIAN92 (94) - reads CSD (cambridge X-ray structural database) - reads and writes the formats (MOPAC-Z matrix, MDL, SMD and PDB files) StrukEd-Lite is available from: Umschau Verlag POB 1247 D-58207 Schwerte (Germany) Fax +49-2304-83271 Phone -81854 (StrukEd is not expensive, DEMO version is available aprox. 20.-DM) For more details you can see the WWW information: http://ibm530.chemie.uni-halle.de/usr/www/software.htm or contact the authors: boegel@chemie.uni-halle.de with best regards Horst From: SMTP%"tamasgunda@www.ccl.net" 14-MAY-1996 08:02:06.91 Subj: CCL:M:Z-matrix generation A solution could be Mol2Mol 3.1 from Cherwell Sci. Publ., Oxford. It is a chemical file conversion utility, and not for drawing, but understands a lot of formats of other programs. If you have a 3D structure created by another modelling program, Mol2mol converts it to a Z-matrix interactively, i.e. you can create different Z-matrices with different formats and by using different algorithms from the same molecule. Tamas 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 ************************************************************************ [Comment: Thanks to Drs. M.Zheng, L.Wilson, J.Brecher, Horst and T.Gunda. The new PC version of CAChe Editor (with MOPAC), CSChem3D and StrukEd-Lite seem to be what I want. Mol2Mol still requires Z-matrix or other written, not drawn, input. The traditional way to generate input, i.e. writing a Z-matrix, is much appreciated but just not efficient at least for me. However, manually altering the Z-matrix is useful so it's best to have the program to go in both ways: Z-matrix <--> picture.]