[gmx-users] Improper dihedrals ordering issue

Hemalatha Jayabal hemalathajayabal at gmail.com
Thu May 10 08:56:58 CEST 2018

Hi all,

I am a beginner in GROMACS. I have a protein in which there is a non
standard amino acid for which parameters are added manually by me from
literature. I am using CHARMM27 force field in GROMACS. I got the topology
by using pdb2gmx. While adding ions to make my system neutral I encountered
an error saying that improper dihedral parameters were not found. On
looking onto the dihedrals, i found that the central atom was 'k' and not
'i' (like the standard gromacs dihedrals). When i checked other dihedrals
without the manually added residue, the central atom was 'i'.

I am confused as to whether the dihedral parameters from ffbonded could be
re-ordered for this case and could be used. (The order mentioned in
topology but parameters for same dihedral in ffbonded)

I hope I am clear regarding my query

Hemalatha Jayabal

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