[gmx-users] More dihedrals generated than provided in the force field & "No default Proper Dih. types" as a result

[Justin Lemkul]

On 12/27/17 9:39 AM, Timofey Tyugashev wrote:
> I'm building a protein with a cubic [Fe4S4] cluster using parameters 
> from a published paper.
> This parameters provide only two dihedral angles types (S-FE-SG-CB and 
> FE-S-FE-SG, where S and FE belong to the cluster and SG and CB belong 
> to the Cys residue).
> GROMACS automatically generates far more dihedrals with types like 
> S-FE-S-FE (looks like all of them are inta-cluster) which are omitted 
> in the source paper and are explicitly stated to be redundant for MD. 
> However  grommp generates errors and stops:
>
> ERROR 49 [file topol.top, line 32916]:
>   No default Proper Dih. types
>
> How to solve this problem?

pdb2gmx automatically generates all possible dihedrals. If they are not 
necessary in your force field description, either remove the offending 
lines from your topology or assign them dihedral parameters with force 
constants equal to zero so they impose no force.

-Justin

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

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