Hi, > 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). I use the -h option, which usually works > fine, but sometimes interprets a -CH2-CH2- group as a -CH=CH- group
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? Best regards, Pascal ------------------------------------------------------------------------------ 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
