![]() ![]() There is currently one limitiation to the -renum flag. Will create a MOPAC input file with atom 9 from myfile.xyz as atom 1 in myfile.dat. Will create a MOPAC input file with atom 1 from myfile.xyz as atom 1 in myfile.dat.īabel -ix myfile.xyz -renum 9 -oai myfile.dat "AM1 MMOK T=30000" If you use -renum X where X is an integer, Babel will use atom X as atom 1 in the Z-matrix.īabel -ix myfile.xyz -renum -oai myfile.dat "AM1 MMOK T=30000" If you use -renum by itself, Babel will use atom 1 in the input structure as atom 1 in the Z-matrix. Renumbering in Babel 1.1 is accomplished using the -renum flag. If this flag is used, Babel will attempt to renumber the structure so that the Z-matrix is contiguous. I've added a new flag, "-renum" to Babel 1.1. Having these "bonds" in your Z-matrix tends to create all sorts of problems during geometry optimization. If atoms are not numbered properly you end up with very long bonds. The Cartesian to internal algorithm goes kind of like this :įind the closest atom with atom number 60 i It is actually brought about by a poorly numbered structure. This is not a bug in the Cartesian to internal algorithm. I have received mail from a number of people who have complained that the Z-matrix created by Babel contains very long "bonds" (often 5 to 10 angstroms). Note the use of the double quotes around the keywords. To perform the above conversion with the keywords PM3 GEO-OK T=30000 in the file mopac.dat the user would enter:īabel -imo mm2.grf -oai mopac.dat "PM3 GEO-OK T=30000" The following output type codes are currently supported.įor example: To convert an MM2 output file named mm2.grf to a MOPAC internal coordinate input file named mopac.dat the user would enter: The -o flag is used to set the output file type. The following input type codes are currently supported. The -v flag is optional and is used to produce verbose output.The -i flag is used to set the input type. The command line input has the following format:īabel -i (in type) (infile) -o (out type) (outfile ) Īll arguments surrounded by are optional. The menu interface can be accessed by typing: Setup babel ( or source /sgi/local/setup/t) The babel program may be invoked using command line options or menus. Gaussian Cartesian Gaussian Z-matrix Gaussian Z-matrix tmplt Mechanicsīabel will write the following file types :Ĭacao Cartesian Cacao Internal CAChe MolStructĬhem3D Cartesian 1 Chem3D Cartesian 2 ChemDraw Conn. Spartan Spartan Semi-Empirical Spartan Mol. GAMESS Output Gaussian Z-Matrix Gaussian Output Babel was written by Pat Walters and Matt Stahl Dolata Research Group Department of Chemistry University of Arizona Tucson, AZ 85721 It will interconvert many coordinate file types.īabel will read the following file types :Ĭambridge CADPAC CHARMm Chem3D Cartesian 1 ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |