On Tue, Feb 10, 2015 at 03:13:34PM +0000, Browning Nicholas John wrote: > Hi All, > > It seems to me that there is a restriction on the number of > atoms (~1000) OB can handle when using mol2 file format. I know > this is also true for SMILES and InChI however this doesn't > make much sense for mol2. > > I currently do mutations/atom manipulations with large proteins > with non-standard residues, so its a requirement that I load > molecules with formally defined bonding. Loading with PDB leads > to incorrect bonding when I attempt to dump out after > modifications. > > Can anyone offer any solutions? > > Nick >
If your PDB files already have correct bonding information then you can skip the bond perception and use preexisting bonding from CONECT records (option b for PDB file). Reinis ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
