# Terminal Residue Handling **URL:** https://gromacs.bioexcel.eu/t/terminal-residue-handling/10286 **Category:** User discussions **Created:** [October 5, 2024, 7:09am UTC](https://gromacs.bioexcel.eu/t/terminal-residue-handling/10286 "2024-10-05T07:09:10Z") **Posts on this page:** 1 **Page:** 1
### Author: ![AnanyaC](https://avatars.discourse-cdn.com/v4/letter/a/8797f3/32.png) [@AnanyaC](https://gromacs.bioexcel.eu/u/AnanyaC) #### Post date: [October 5, 2024, 7:09am UTC](https://gromacs.bioexcel.eu/t/terminal-residue-handling/10286/1 "2024-10-05T07:09:10Z")
GROMACS version: GROMACS modification: Yes/No I am trying to create an .rtp file for modified protein residues in amber99sb.ff When trying to create a topology it throws an error which looks like this: Processing chain 3 ‘A’ (1103 atoms, 139 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 240 donors and 189 acceptors were found. There are 276 hydrogen bonds Will use HISE for residue 3 Will use HISE for residue 43 Will use HISE for residue 117 Identified residue GLY1 as a starting terminus. Identified residue ALA139 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS3 MET4 HIS43 MET94 CYS100 CYS114 HIS117 NE216 SD25 NE2309 SD745 SG788 SG898 NE2919 MET4 SD25 0.959 HIS43 NE2309 2.872 2.702 MET94 SD745 6.202 5.697 3.706 CYS100 SG788 5.761 5.113 3.585 1.183 CYS114 SG898 5.098 4.295 3.454 3.006 1.981 HIS117 NE2919 5.042 4.222 3.649 3.746 2.776 0.811 MET124 SD975 4.162 3.317 2.977 3.326 2.311 1.159 1.487 * * * Program: gmx pdb2gmx, version 2022.3 Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1081) 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). How to deal with this error. Any comment it appreciated.