I think you have capped your residue in the N-terminal and C-terminal end...and the capping is not defined in your .rtp entry.. that's why this error is coming
On Tue 12 Nov, 2019, 3:58 PM shakuntala dhurua, <madhu.dhuru...@gmail.com> wrote: > hello, > Here I want to generate arg.pdb to arg.gro by using amber99sb force field . > for test i have used 1 residue of arginine but i got Fatal error: > There is a dangling bond at at least one of the terminal ends and the force > field does not provide terminal entries or files. Fix your terminal > residues so that they match the residue database (.rtp) entries, or provide > terminal database entries (.tdb). and following is the attach pdb format > which i have used for pdb2gmx ,please suggest me to solve this problem > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.