On Sat, Apr 13, 2013 at 10:42 AM, vidhya sankar <scvsankar_...@yahoo.com>wrote:
> Dear Justin thank you for your reply, > Is there is > Any tool to merge topology of CNT (generated by g_x2top tool) and Cyclic > Peptide ( created by pdb2gmx) . otherwise Mere copy and Pasting the > Corresponding Entries of CNT ( atom, Bond ,Angle, Dihedral Section) to > topology of Cyclic peptide > > Also Should i Combine .RTP of CNT & .RTP of Cyclic Peptide for My system > (My system CNT wrapped By cyclic Peptide ) > > How to combine ? > > Mere Coy and Editing ( Changing Number and Oder) and put it .RTP data > base > > Any topology can be included in a .top if it is converted to an .itp file by removing the force field #include statement, [system] directive, and [molecules] directive. Then just #include the new .itp file. This is effectively what every pdb2gmx-generated topology does with ions, water, etc. You have a CNT, which can be viewed as just another solute in the system, so just #include its parameters after proper conversion from .top to .itp. -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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
