Feature Requests item #871696, was opened at 2004-01-06 09:47 Message generated for change (Comment added) made by rkanters You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=871696&group_id=23629
Category: New IO Format Group: None Status: Open Priority: 5 Submitted By: Egon Willighagen (egonw) Assigned to: Nobody/Anonymous (nobody) Summary: A Z-matrix Guassian input file Reader Initial Comment: See CDK RFE #871694. ---------------------------------------------------------------------- Comment By: Rene Kanters (rkanters) Date: 2004-10-13 06:45 Message: Logged In: YES user_id=905185 Actually z-matrices in Gaussian input (or some other programs for that matter) can be a bit trickier in that they may have variables and constants in their definitions, e.g., X X 1 rx C 2 rc 1 a90 C 2 rc 1 a90 3 t180 H 2 rh1 1 a1 3 t0 H 2 rh2 1 a2 3 t180 H 2 xh 3 a3 1 t180 Br 2 xbr 3 a4 1 t180 variables rc 0.60002733 rh1 1.66512683 rh2 1.66512683 a1 89.62647357 a2 89.62647357 xh 2.47262334 xbr 3.90355994 a3 90.0 a4 90.0 constants rx 1.0 a90 90.0 t180 180. t0 0. which makes interpreting a bit trickier (they actually also can have things like -a3 in them...). I would suggest, since the question was about Gaussian input files, to use Gaussians newzmat tool to convert the input z-matrix to something like an xyz file, with the format: newzmat -izmat infputfilename.com -oxyz outputfilename.xyz The only thing is that you will loose your dummy atoms, since Gaussian strips those from its cartesian output (both in regular output and in newzmat output). I hope this helps. Ren� ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-09-29 09:57 Message: Logged In: YES user_id=1050060 OK, I have a basic understanding of internal coordinates. But I thought that you started off with a couple of real points (and perhaps an artificial point) and went from there. I do not understand anything about the Z-matrix representation. ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2004-09-28 08:31 Message: Logged In: NO z-matrix means internal coordinate used by the mopac or the gamess etc. ------ C O 1 1.2000 H 1 1.1000 2 120.0000 C 1 1.5000 2 120.0000 3 180 H 4 1.1000 1 110.0000 2 0 H 4 1.1000 1 109.9999 2 -120.0000 H 4 1.1000 1 109.9999 2 120 ------ ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-05-26 03:21 Message: Logged In: YES user_id=1050060 Egon, Is this done? I am not sure what you mean by 'Z-matrix' Miguel ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=871696&group_id=23629 ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
