Dear Pascal and Geoffrey, Thanks for your replies!
>Well, you posted this to the openbabel mailing list Right. Is that a problem? >and got an answer there too. Unless it's really a file from the Protein Data >Bank (with actual atom names), PDB files are not a good interchange format. On Feb 18, 2011, at 10:14 AM, Pascal Muller wrote: > pdb doesn't contains information about bond type... Seems that the > simulation shortened the bond... As far as I know, the only way to > determine bond type in a pdb file is the bond length. > >> and >> adds only 2H instead of 4. Is there a way to correct this? For example, >> can I tell babel explicitly to treat a C-atom as sp3, and not as sp2? > > Does your software generate output in e.g. mol2? The software should > know the atom/bond type, isn't it? Well, the software is written by myself; of several formats I tried, 'pdb' just happened to be the first one which added any hydrogens at all with the -h option. With some other formats, like 'xyz' or g03 log, nothing was added at all. Don't know if that's intended or not. Thanks for the tip with 'mol2', I'll try that; from the description this seems to be what I need. > Why not include hydrogens before the simulation? That would be the easiest option, but the guy who did the simulation tells me that the explicit H force fields he can use do not have parameters for some of the atoms in these molecules. >I agree completely with Pascal. Try mol2 or mol/sdf if you want to retain atom >types. Otherwise Open Babel has to "perceive" bond orders and without >hydrogens to complete the valence, we have to base hybridization on bond >lengths and angles. It's good, but not fool-proof. -------------------------------------------------------------------- myhosting.com - Premium Microsoft® Windows® and Linux web and application hosting - http://link.myhosting.com/myhosting ------------------------------------------------------------------------------ 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
