1. Atoms 0 does not have atomic number needed for QMMM. Check atomtypes section in you topology or forcefield.
mising atomic number parameter in top file.
mandatory |
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atom type; bonded type; atomic number; m (u); q (e); particle type; V\(^{(cr)}\) ; W\(^{(cr)}\) (bonded type and atomic number are optional) |
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those two parameters are not necessary for MD simulation, but must exist for CP2K setup.
2. The missing vdW should be added for OH and HW in amber force field. (see from https://www.cp2k.org/howto:biochem_qmmm)
Before running the QM/MM simulation we need to amend our prmtop file, because in the classical forcefield, several hydrogen atom types do not have separate Lennard-Jones parameters or they are set up to 0.0. The AMBER FF atom types are HO (from the TIP3P water model), HG (from serine, threonine and tyrosine residues). This will cause unphysical interactions with the QM region and the simulation will fail due for stability reasons. The hydrogen atoms with these atom types will strongly interact with the QM electron clouds, eventually crashing the system. To prevent this from happening, we have to add the correct LJ parameters to the mentioned atom types using the ambertools utility parmed.
$ parmed complex.prmtop changeLJSingleType :WAT@H1 0.3019 0.047 changeLJSingleType :*@HO 0.3019 0.047 outparm complex_LJ_mod.prmtop quit