[gmx-users] More dihedrals generated than provided in the force field & "No default Proper Dih. types" as a result
jalemkul at vt.edu
Wed Dec 27 19:46:49 CET 2017
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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