[gmx-users] Improper dihedrals ordering issue

[Justin Lemkul]

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

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

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