Dear Obenbabel community, I am new in using Openbabel. I have an .xyz file produced by GAUSSIAN ( H2O2.xyz <http://forums.openbabel.org/file/t375678/H2O2.xyz> ). This file includes a DNA double helix of 5 base pairs surrounded by hydrogen peroxide molecules. My goal is to analyze some double-helical parameters of DNA in 3DNA software package. This software requires a .pdb file in which DNA atoms are labeled in *canonical form* (N1,C2,...). But when converting my .xyz file to .pdb using Openbabel, in an output file there is only an information about the type of atom (N,C,O,...) - H2O2_new.pdb <http://forums.openbabel.org/file/t375678/H2O2_new.pdb> . Due to that it cannot be recognized by 3DNA program. To make a conversion I use the command: obabel -ixyz H2O2.xyz -opdb -O new/H2O2_new.pdb
Could you tell me please if there is a possibility in Openbabel to create a .pdb file with a canonical labeling of atoms? Thanks in advance. Best regards, Oleksii -- Sent from: http://forums.openbabel.org/General-discussion-f3090658.html _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
