[gmx-users] Improper dihedrals ordering issue

Justin Lemkul jalemkul at vt.edu
Thu May 10 14:06:30 CEST 2018

On 5/10/18 2:56 AM, Hemalatha Jayabal wrote:
> 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)

Don't re-order existing parameters. Make the ones you have added conform 
to the required format.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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