| 5:10:44 AM PDT - Thu, Apr 26th 2018 |
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As I said before, you have atoms too close together because of the occupancy field in the PDB file. To quote the Guide to Understanding PDB Data (https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/dealing-with-coordinates):
"Macromolecular crystals are composed of many individual molecules packed into a symmetrical arrangement. In some crystals, there are slight differences between each of these molecules. For instance, a sidechain on the surface may wag back and forth between several conformations, or a substrate may bind in two orientations in an active site, or a metal ion may be bound to only a few of the molecules. When researchers build the atomic model of these portions, they can use the occupancy to estimate the amount of each conformation that is observed in the crystal. For most atoms, the occupancy is given a value of 1, indicating that the atom is found in all of the molecules in the same place in the crystal. However, if a metal ion binds to only half of the molecules in the crystal, the researcher will see a weak image of the ion in the electron density map, and can assign an occupancy of 0.5 in the PDB structure file for this atom. Occupancies are also commonly used to identify sidechains or ligands that are observed in multiple conformations. The occupancy value is used to indicate the fraction of molecules that have each of the conformations. Two (or more) atom records are included for each atom, with occupancies like 0.5 and 0.5, or 0.4 and 0.6, or other fractional occupancies that sum to a total of 1."
To resolve this you need to look for a script/program someone else has written to automatically extract just one of the positions for atoms with occupancy less than 1, write a script yourself to do it, or manually delete the duplicated atoms from your input. In doing this manually, NWChem could be used as a guide since the code will tell you which atoms are too close to each other.
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