> 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?
You can write out an arbitrary number of digits, e.g. with XYZ. If you want an existing format in Open Babel, I'd suggest DMol3, which I think uses 14 decimals (albeit in Bohr). > 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? No, obfit takes one molecule and fits it onto another, e.g. obfit molecule1.xyz molecule2.xyz >newfile.xyz http://openbabel.org/wiki/Obfit > Besides, I wish all atoms could be used in the alignment. Which SMILES > should I use? You'd pick a SMARTS that corresponds to the molecular SMILES. So, for example, if you wanted to superimpose two benzenes: c1ccccc1 Hope that helps, -Geoff ------------------------------------------------------------------------------ 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
