> 1. is it possible to generate the full set of rotamers ( any specified > amount) rather then one with the lowest energy? If ansew to my question is > yes, then HOW???? Can I ask f.e about structures of top 100?
> 2. by default. this program calculates # of rotatable bonds and # of > rotamers. Do you know how to save that information in file??? I have 5000 > molecules, and before starting actual generation of rotamers( and selection > of the one with the lowest energy) i need to know how many i want the program > to generate. It would be useful to know to use with obconformer. For #1, I'd suggest a different program. You can get these through the babel interface: > Typical usage: obabel infile.xxx -O outfile.yy --conformer --nconf > options: description > --log output a log of the energies (default = no log) > --nconf # number of conformers to generate > forcefield based methods for finding stable conformers: > --systematic systematically generate all conformers > --random randomly generate conformers > --weighted weighted rotor search for lowest energy conformer > --ff # select a forcefield (default = MMFF94) > genetic algorithm based methods (default): > --children # number of children to generate for each parent (default = 5) > --mutability # mutation frequency (default = 5) > --converge # number of identical generations before convergence is > reached > --score # scoring function [rmsd|energy] (default = rmsd) So you might want something like: # use the genetic algorithm method obabel infile.sdf -O outfile.sdf --conformer --nconf 100 --score energy # or use the mmff94 with weighted searching obabel infile.sdf -O outfile.sdf --conformer --nconf 100 --weighted For #2, you'll want to save the output to a file. On Linux or Mac, you can do something like this: obconformer file.sdf 2>>log.txt Then log.txt will have the information you request. (You can read more about shell scripting to automate this further.) Hope that helps, -Geoff ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
