Thanks for your Reply. If I comment the WeightedRotorSearch, the extended conformation of the peptide is indeed conserved, but there isn't any new conformer of the backbone generated, and I want to create new conformers of the small loop between the ends of the peptides. I thought that WeightedRotorSearch could create new conformers and Minimization could refine this structure in order to fit the geometrical constaints. But probably there are too much energetical barriers to be overcome and minimization can't deal with it. A montecarlo rotational refinement would be more suitable. I don't think OB can do it? Regards François
----- Original Message ----- From: "Geoffrey Hutchison" <ge...@geoffhutchison.net> To: "françois Bagaïni" <bagaini...@dbmail.com> Cc: <openbabel-discuss@lists.sourceforge.net> Sent: Friday, October 08, 2010 8:39 PM Subject: Re: [Open Babel] Build conformers of a loop. On Oct 6, 2010, at 9:42 AM, françois Bagaïni wrote: > But When I fit the Nterminal ends of both molecules (initial conformer and > the result of the program), the C-terminal end is not superimposed. It > looks as if minimization can't deal with geometrical constraints. What's > wrong in my program? Are you sure it's the minimization and not the WeightedRotorSearch call which has problems? I just tried what you asked in Avogadro (which uses OB for force fields and minimization) and I had no problems with freezing atoms for minimization. I'm just not sure that the conformer search handles constraints -- and I think that's where your problem is. What happens if you comment out the WeightedRotorSearch call? -Geoff ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
