From jkl@ccl.net Fri Mar 5 06:11:12 1993 From: Jan Labanowski Date: Fri, 5 Mar 1993 11:11:12 -0500 Message-Id: <199303051611.AA07016@krakow.ccl.net> To: chemistry@ccl.net Subject: Archives off for the weekend Dear subscribers to Comp.Chem.List The archives of CCL will be unavailable on the weekend, since the computers will be down for the weekend (some building maintenance work). If you need something from the archives, do it today. To those who did not read the help file, the archives are available via anonymous ftp (on www.ccl.net, 128.146.36.48) or via e-mail interface at OSCPOST@ccl.net. For example, if you want to retrieve a "help" file for the list do: ftp www.ccl.net Login: anonymous Password: Your_email_address ftp> cd pub/chemistry ftp> get help ftp> quit or send a message: send help from chemistry to OSCPOST@ccl.net and the help file will be forwarded to your mail box. As some of you know, there are many useful things in the archives, starting from positions.offered and positions.wanted files and ending on documentation, software, and overviews. The archives can also be searched for keywords. To find out how to search the archives retrieve file help.search (substitute help with help.search in the example given above). Have a good weekend. Jan Labanowski Administrator of CCL. Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From jkl@ccl.net Fri Mar 5 09:06:45 1993 From: Jan Labanowski Date: Fri, 5 Mar 1993 14:06:45 -0500 Message-Id: <199303051906.AA07281@krakow.ccl.net> To: chemistry@ccl.net Subject: Archive off NEXT weekend It is the CCL Bureaucrat again, Sorry for missinfo. The archives of CCL will be off next weekend. Change of plans. You now have one week lead time {:-)} Jan jkl@ccl.net Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From hogue@mosquito.den.mmc.com Fri Mar 5 07:52:50 1993 Date: Fri, 5 Mar 93 14:52:50 MST From: hogue@mosquito.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9303052152.AA03277@mosquito.den.mmc.com> To: chemistry@ccl.net Subject: hydrazine I recently posted an excessively long N-N bond length for hydrazine and erroneously attributed this to AM1. It turns out to have been the optimized bond length produced by MNDO, for which I appologize and post the following: HYDRAZINE OUTPUT Method MNDO AM1 configuration closed closed N-N length 2.698A 1.357A N-H length 1.000 1.030 HOMO energy -.3032h -.3767h LUMO energy -.1234h .1182h dipole moment 2.68 2.268 electronic polarizability 7.89 3.438 charge on N -.2 -.25 charge on H +.1 +.11 Wiberg index N-N .959 1.037 Wiberg index N-H .96 .955 Binding energy kcl/mole -253.5 -418.4 Heat of formation " 180.9 16.0 (big difference) N-N bond energy -.067h -.562h " " N-H bond energy -.47h -.478h h=hartree Pat Hogue From chs1nt@surrey.ac.uk Fri Mar 5 17:08:50 1993 From: Dr Nicholas P Tomkinson Message-Id: <9303051708.AA15823@central.surrey.ac.uk> Subject: Connoly MS program To: chemistry@ccl.net Date: Fri, 5 Mar 93 17:08:50 GMT Hi, does anyone know if I can get hold of the Connoly MS program without having to wait for it to arrive from QCPE? I am using Dock 3.0 (Kuntz et al.) and had assumed that since the fortran code of QUANTA's MS program refers to it as a derivative of Connoly's program, that it would give the same format file. This is apparently not so since Dock 3.0 can not handle it (REFORMATMS in Dock cannot read it either.) Maybe someone has used Dock with QUANTA and can give me some help? Cheers Nick Tomkinson From shenkin@still3.chem.columbia.edu Fri Mar 5 15:16:23 1993 Date: Fri, 5 Mar 93 20:16:23 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9303060116.AA24476@still3.chem.columbia.edu> To: mmodinfo@uoft02.utoledo.edu, chemistry@ccl.net, dibug@comp.bioz.unibas.ch Subject: Query re: PDB files I am cleaning up some of the PDB file handling for MacroModel, and I am seeking advice from the readership on several issues. For various arcane reasons, it will be easier for me to produce PDB-style files if I'm a little careless about atom order; when there are H's in the file, some of them might precede the heavy atoms in a given residue. Aside from this, the files ought to be "standard:" that is, the atom names and numbers and residue names and numbers should be correct, CONECT and TER records will be present, and the atoms in each residue will be together in the file. Also, the heavy atoms will be in the expected order. The question is: will this departure from normal practice break any programs that you know of that use PDB files? Of course, another way to go would be to delete any hydrogens; but there are enough "real" PDB files that contain them that presumably most PDB-reading programs know what to do with them. Assuming I do keep hydrogens in, do you think I should also keep lone pairs in, where these are explicit (as in lone pairs on Sulfur for the AMBER force-field)? As it is now, I am leaving them there, and naming them the same way H's are named, but replacing the H with an L. Here there are two issues: (1) whether some programs that read PDB files will recognize the lone pairs; (2) whether this will break programs that do not recognize lone pairs. Curious in the Bronx, -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************ Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ***************** Watch this space for an important message *****************