[gmx-users] Unknown bond_atomtype CAY

Sameer Edirisinghe nootsam at gmail.com
Sun Sep 18 18:30:07 CEST 2016

Dear users,
There is one thing i cannot clarify from gromacs manual which is about
following error occurred while running grompp

Fatal error:
Unknown bond_atomtype CAY

 I used to create .rtp file from atom types which are already defined in
 atomtype.atp file. But still above error occurring while running grompp.
Not sure should i add again thes atoms to atp file and if so how to add
them. Part of my rtp file is as below, I have modified the ffbonded.itp
(only bond types added) successfully.

[ bondedtypes ]
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
  1      1       3          1

[ MD ]
 [ atoms ]
CAY opls_135  0.000  1
CAX opls_135  0.048 2
CAW opls_135  0.047 2
CAV opls_135  0.144 2
OAU opls_154 -0.112 2

Your little help is much appreciate for this.

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