> I need to add Hydrogens to a large number of pdb-files, which all > contain the same molecules in different configurations (the results of > molecular simulation run with implicit hydrogens). I use babel with the > 'add hydrogen' option, which usually works fine, b
Well, you posted this to the openbabel mailing list 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? > Why not include hydrogens before the simulation? 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. Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ ------------------------------------------------------------------------------ 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
