Also, if you have specified the bond in .top file properly then gromacs should consider a bond there. Run some MD to see if the bond stays intact...
On 2012-09-22 02:23:13PM +0800, vidhya sankar wrote: > Thank you Sir. For your repl > > > I Would like to construct .top file for Cyclic Peptide . > My N-terminal residue is ARG and C-Terminal is > PRO . In pdb There is Bond between N atom of ARG (First residue) and C > atom of PRO (Last Residue) When I Generated Topology using pdb2gmx . But > there is No bond connectivity Between First and Last Atom .Then > Manually I have Edited .top file and I have defined the bond Between > First Atom (1) and Last atom (169) . Then I have done EM Successfully . > My Question Is > > Will This Manual Editing of .top File create a bond or Not . > > With Regards > S.Vidhyasankar > -- > 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
