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