z-matrix is internal coordinates: http://www.cup.uni-muenchen.de/oc/zipse/lv18099/internal.html http://www.chem.swin.edu.au/modules/mod5/zmatrix.html http://www.chem.swin.edu.au/modules/mod5/z_samples.html http://home.iitk.ac.in/~nsath/z-matrix.html
note that the following is VERY NONSTANDARD I think: http://www.chm.tu-dresden.de/edv/vamp65/BASICS/vb_02f.htm I don't know if the intent is to accept z-matrices that involve variables or not. That's a question to ask. For the molecule below: > C placed at 0,0,0 > O 1 1.2000 placed at 1.2,0,0 > H 1 1.1000 2 120.0000 placed at x,y,0 such that position from atom 1 (C) is 1.10 angstrom, and angle H 1(C) 2(O) = 120 degrees > C 1 1.5000 2 120.0000 3 180 placed at x,y,z such that position from atom 1 (C) is 1.5 angstroms, angle C 1(C) 2(O) is 120 degrees, and dihedral angle (cw -- I think) of 180 degrees. > H 4 1.1000 1 110.0000 2 0 placed at x,y,z such that position from atom 4 (C) is 1.10 angstroms, angle H 4(C) 1(C) is 110 degrees, dihedral H 4(C) 1(C) 2(O) is 0 degrees. all lines after this are like the previous. NOTE however: a) Sometimes one or two "phantom atoms" are used, usually written "X" or "XX" just to get the ball rolling. These aren't atoms, just starting points. b) You must parse line 3 carefully. Some implementation Bob > Feature Requests item #871696, was opened at 2004-01-06 06:47 > Message generated for change (Comment added) made by nobody > 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: Nobody/Anonymous (nobody) > Date: 2004-09-28 06:31 > > 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 01:21 > > 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 > ------------------------------------------------------- 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
