On 01/16/2011 07:54 PM, Geoffrey Hutchison wrote: >> The following informations could be useful: >> 1) I exported the file directly from Material Studio >> 2) The problem seemsto be size dependent, i.e. conversion works if I cut >> down the structure to 150 atoms >> > I suspect this isn't a specific problem with "car" format, rather with > bond/aromaticity perception in systems with lots of fused rings. So if you're > looking at a zeolite or diamondoid structure, for example, the computational > time goes up dramatically. > > You can short-circuit this. For example, since you're converting to XYZ, you > don't need the bonds: > > babel -H car > car Accelrys/MSI Biosym/Insight II CAR format > Read Options e.g. -as > s Output single bonds only > b Disable bonding entirely > > So what you'd want to do is something like this: > > babel file.car -ab file.xyz > > This will convert from CAR to XYZ without attempting bond perception. (I > suspect the slow part isn't bond perception, rather the default option of > attempting to perceive multiple bonds.) > > Hope that helps, > -Geoff
Dear Geoff, to other users knowledge, I just tried it out again following your suggestion, and you were right. Thanks for your help Gabriele ------------------------------------------------------------------------------ The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
