On Wed, Apr 10, 2013 at 8:56 AM, vidhya sankar <[email protected]>wrote:
> Dear Justin , Thank you for your reply, > I need > to construct Topology For Carbon Nano tubes (CNT) in gromoff53a5.ff . > > For that When i run the Following Command > > ./g_x2top_d -f CNT.gro -o CNT.top -r CNT.rtp > > I have got Error as follows > Can not find forcefield for atom N-325 with 0 bonds > Can not find forcefield for atom CA-326 with 2 bonds > Can not find forcefield for atom CB-327 with 2 bonds > Can not find forcefield for atom CG-328 with 2 bonds > Can not find forcefield for atom C-330 with 2 bonds > Can not find forcefield for atom O-331 with 1 bonds > Can not find forcefield for atom N-332 with 0 bonds > The preceding lines appear to belong to a protein residue. Don't use g_x2top for proteins. That's what pdb2gmx is for. > Can not find forcefield for atom C-836 with 3 bonds > Can not find forcefield for atom C-837 with 3 bonds > Can not find forcefield for atom C-838 with 2 bonds > Can not find forcefield for atom C-839 with 2 bonds > Can not find forcefield for atom C-840 with 3 bonds > Can not find forcefield for atom C-841 with 3 bonds > Can not find forcefield for atom C-842 with 2 bonds > Can not find forcefield for atom C-843 with 2 bonds > > Could only find a forcefield type for 321 out of 843 atoms > > > How to solve it ? > You need a suitable .n2t file. For a CNT, it is trivial to create the necessary entry since the geometry is regular. Please consult the manual and website. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
