Molecular visualization programs determine bonds through distance measurements. Especially since .gro files do not contain connectivity information. The topology is where the bond infomration is stored. So check there...
On 2012-09-22 12:33:31PM +0800, vidhya sankar wrote: > > > Dear Justin Thank you for your Reply > > After pdb2gmx When i Visualize the resultant .gro file of my cyclic peptide > in VMD > > I have Observed the Bond Between Nitrogen atom (N ) of First residue and > Carbon atom (C) of Last residue I have not observed The same bond when I > open and Visualize in Chimera . Then How Could i Confirm Whether the bond is > present or Not? > > Thanks in Advance > > -- > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
