[gmx-users] Unknown bond_atomtype

Nash, Anthony a.nash at ucl.ac.uk
Wed Feb 17 17:26:56 CET 2016

Hi all,

As per a previous email (cross linking two peptide chains), I¹ve created a
brand new crosslink (think disulphide bond) residue from scratch. I have
defined it in all the files necessary (.rtp, residuetypes, specbond,
atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no

Unfortunately when I run grompp (5.0.4) I get the following error:

Fatal error:
Unknown bond_atomtype MN1 <‹‹ first atom in my new residue

At first I thought my topology might be pointing to the wrong forcefield,
but I¹ve checked and double checked:

#include "/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
#include "modic.itp"
;#ifdef POSRES
;#include "posre.itp"

[ system ]
; Name
MODIC with glycine terminal ends

[ molecules ]
; Compound        #mols
MODIC             1

I¹m going to take a guess at what the problem is. Each of the atoms in the
residue was derived from scratch.Therefore, they have a completely new
type. I wasn¹t feeling very creative with my naming convention so the atom
name and the atom type are identical e.g.,

;MODIC crosslink
[ MOD1 ]
 [ atoms ]
MN1     MN1     -0.3640         1
MC1     MC1     0.0358          2
MC15    MC15    0.4871          3


Will this have confused grompp?

Many thanks

Dr Anthony Nash
Department of Chemistry
University College London

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