From: <ha...@st...> - 2004-09-28 19:39:35
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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 > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > |