[gmx-users] dihedral not created even with ffbonded.itp all set

MD refmac5 at gmail.com
Mon Jan 1 14:36:22 CET 2018

Hi Gromacs folks,

I was trying to combine protein with an arbitrary ligand for simulation. I
think there are two routes to go, one is to create the protein.gro and itp
with gmx and search the ligand topology on atb or elsewhere, and combine
them together manually for further simulation. The other is to add topology
parameters into ffbonded.itp, merged.rtp and use gmx to create the
ligand.itp file.

I chose to go with the second route and added the bond, dihedral angles
parameters into the ffbonded.itp and made sure the names and types are
consistent in merged.rtp, but the ligand.itp I got from gmx had no
parameters at all. I had made sure all the names match among pdb,
merged.itp and ffbonded.itp. Can anyone tell me what could be the problem

Another quick question is regarding the first route, say I went with the
first route, I will be able to obtain the ligand.itp from atb, but is there
also a quick way to convert the ligand.pdb to ligand.gro easily? I used atb
but it only gave back the pdb format back and I will need to manually
change the sequence of the parameters in a txt file.

Thank you and happy new year.


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