Dear Justin Thanks Again for your reply When I run Pdb2gmx using -ter option for my Cyclic peptide and i have selected None for both termini as you instruct in the previous mail i have got error as follows
Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. How to resolve these error For you remembrance i have pasted the previous mail Discussion I am doing MD Cyclic Peptide When I run pdb2gmx , The Conect Infromation in pdb file are ignored . so that it is not able to connect the first and last residue in cycle . But it construct and .top and.gro files successfully while in .gro file the end residues are closed as NH3+ and COO-(charge) (it means there is Bond between Nitrogen and carbon atom) > > It consider the N atom of first residue as NH3+ and C atom as COO-(charge) but I need to take N as peptide Nitrogen and C as Peptide carbon > > What Should i do to invoke conect information when i run pdb2gmx tool Use the -ter option and choose "None" for both termini.( Your Ansewr) > Also Can i Directly Edit (it means removing excess hydrogen and oxygen atom by ; symbol) .top an .gro files and can i use to proceed further ? No. This will cause errors in the [moleculetype] numbering and all successive (Your Answer) directives. Re-run pdb2gmx instead. Thanks in Advance 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
