Dear All, I have two small molecules that are identical. One geometry is the ground state and the other is the first excited state. I have their fchk file, from gaussian 09. I am trying to figure out how to superimpose these two molecules using open babel. The catch is: I wish I could loose accuracy as minimum as possible. I mean, I wish I could extract the two geometries from the fchk file keeping as many decimal digits as possible and then generate two new geometries with as many decimal digits as possible. How can I do it? Which format allow me to use the largest number of decimal digits?
I have looked into the obfit code but I have another question. How the two molecules should enter? One after the other? Any separation? just cat molecule1 molecule2 > moleculefit? Besides, I wish all atoms could be used in the alignment. Which SMILES should I use? Thank you in advance, Demetrio -- View this message in context: http://forums.openbabel.org/Superimposing-two-molecules-tp4656327.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with <2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
