Dear justin , Thank you fro your Reply
I am doing MD for Cyclic poly Peptide With ARG as N-termina and PRO as C-terminal . I have run pdb2gmx it is oak. . I have solvated and added ions successfully But when i Run the Energy Minimization The Bond between N atom of ARG and C atom of PRO is broken . What Should i Do To keep this Bond Through entire EM and MD ? Can i Use Constraints option in topology file if i need to use Constraints option What is the Syntax ? Also The Bond is not constructed between N atom and C atom of terminal ARG and PRO residues in Topology -- 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
