Dear Justin and other Gromacs users , Thank you for your previous reply Again i Have tried the option -missing when i use pdb2gmx tool i have got errror as follows My command is
./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -p 2KDQ.top -missing -ignh -ter There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. I went through a Mailing Archive Yet no body explain the proper Topology construction for cyclic peptide It Discussed about Manual editing of topology But in my case it is headache Because my cyclic peptide contains large number of atom How to solve this problem without manual editing 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
