From chemistry-request@ccl.net Sun Apr 21 19:10:11 1991 Date: Sun, 21 Apr 91 17:50:34 -0400 From: bbesler@vela.acs.oakland.edu (Brent H. Besler) To: chemistry@ccl.net Subject: Mopac 6.0 debacle Status: RO In order to hopefully clarify the the great Mopac 6.0 for Unix debacle(and hopefully alleviate it), I have set up the following directories on ouchem.chem.oakland.edu(141.210.108.5). Please read the descripions befor downloading. pub/mopac50esp - The Mopac 5.0 ESP code of Besler, Merz, and Kollman. There are three makefiles for the Ardent, Convex, and Silicon Graphics Iris systems. The Mopac 5.0 tests have not been run on this code! pub/mopac50tests - The verification tests for Mopac 5.0 from QCPE pub/mopac6bbport - My port of the Vax Mopac 6.0 from QCPE to a DEC Ultrix 3100 workstation. The is the early untested port. No code except the timing routine was modified(second.f). pub/vax - The original distribution tape of Mopac 6.0 for the Vax from QCPE. pub/ultrix_certified - The files obtained from Jim Stewart in early March 1991, which should be a functioning DEC 3100 Ultirx version. The verification tests(The .dat files and .out files for Mopac 6.0) and all of the manual(documentation files) should be there. There is no Makefile, but the one from the bbport directory should work. Whatever you do, use static memory allocation(not stack allocation). All of the files in the above directories are contained in compressed tar files in the pub directory. For example the files in the pub/vax directory are contained in vax.tar.Z in the pub directory. All of the files are available for anonymous ftp download from ouchem. I will contact Jim Stweart to find out what the true "certification deck" for Mopac 6.0 is. I would recommend using the vax version of Mopac 6.0 as the "true" value. The published heats of formation and geometries in the various J. Comput. Chem. papers of Stewart and the March 1990 Journal of Computer Aided Molecular Design are sources of large amount of published results of Mopac. From chemistry-request@ccl.net Sun Apr 21 19:50:46 1991 Date: Sun, 21 Apr 91 17:54:51 -0400 From: bbesler@vela.acs.oakland.edu (Brent H. Besler) To: chemistry@ccl.net Subject: Documentation for Mopac 5.0 ESP Status: R The documentation for Mopac 5.0 ESP is located in the pub directory of ouchem in the file mopac50espdocs.word4. The files is a Microsoft Word 4.0 for the M Mac binary files. You have to FTP it onto a Mac in MacBinary mode to get it to appear as a Word 4.0 file correctly. From chemistry-request@ccl.net Sun Apr 21 22:39:28 1991 Date: Mon, 22 Apr 91 11:53:27 +1000 From: apa@ccadfa.cc.adfa.oz.au (Alan P Arnold) To: chemistry@ccl.net Subject: Dynamics/Minimisations with Amber 3.0 Status: R I am currently using Amber 3.0 on a Personal Iris to investigate the effects of metal ions on the conformations of small histidine- containing peptides. I would like to generate a large number of 'high-energy' conformations by heating my molecules with Amber's MD program, and save the coordinates at various times during the dynamics projectory, then use these as starting conformations for MIN runs. How do I do this ? I've tried setting NTWX in the MD input (to say, 100 to get coordinates written every 100 steps) but they are all appended into one big file, and what's worse, in a different format to the coordinate file that is required by MIN as input! If anyone has a shell script to automate this procedure of 'dynamics.. saving coordinates..minimisation' I would very much appreciate a copy. Thanks. ---- Alan Arnold | Phone: +61 62 68 8080 Chem. Department,University College | ACSNET: apa@ccadfa.oz Australian Defence Force Academy | UUCP: ...!seismo!munnari!ccadfa.oz!lpb CANBERRA ACT 2600 Australia | ARPA: apa%ccadfa.oz@SEISMO.CSS.GOV