I think it would help significantly if you shared the PDB file you're trying to use and what format you're trying to export to (.. I guess lpmdat for LAMMPS?)
It's very hard to know what atoms, dihedrals or atoms may be missing for you (or why) without the actual data. Thanks very much, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ On Feb 19, 2014, at 9:20 AM, Baki Aksakal <aksakalb...@gmail.com> wrote: > I am trying to obtain the coordinates, angles, and dihedrals and so on of > silk bdp file by using open babel. Although it says 945 atoms and convert and > give the coordinates of 449 atoms and does not give any dihedrals and angles. > there is missing angles and atoms. How can I solve this problem and obtain > the conversion of pdp file correctly into Lammps format. > > > > ------------------------------------------------------------------------------ > Managing the Performance of Cloud-Based Applications > Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. > Read the Whitepaper. > http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk_______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Flow-based real-time traffic analytics software. Cisco certified tool. Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports. Network behavioral analysis & security monitoring. All-in-one tool. http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
