On 4/26/20 1:57 PM, Paolo Costa wrote:
Dear Gromacs users, within Amber99 force field I created a new molecule, polyoxometallate, by creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters from known works, while the parameters for the bonding interactions I determined by Gaussian together with VFFDT software. I did not insert any parameters for the dihedral angles since the VFFTDT software does not calculated them. However as written in the related paper (J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation related to metals can often be ignored".* Does somebody knows how to overcome such error in Gromacs?
pdb2gmx generates all possible angles and dihedrals, as determined by the bonds that are defined in the .rtp entry. Thus, you likely have dihedrals in the topology in which one of the participating atoms is the metal. You have to have parameters for all defined interactions, but it is true that dihedral terms are not typically used in this case. The simplest solution is to define dihedrals with zero force constants so they do not contribute to the forces in the system.
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