[modeller_usage] HSE problem solved, new question

Dear modellers,

two days ago I posted a message about the problem to define Histidine residues with the proton at NE2 instead of ND1. Meanwhile I found out that this can be done by patching the HIS residue with HS2 like this in the special_patches subroutine:

PATCH RESIDUE_TYPE = 'HS2', RESIDUE_IDS = 'His number'

Now I would like to ask some questions on the content of the *.log modeller output file:

o I include some conserved water molecules in my model. This leads to the warning: iatmcls_286W> MODEL atom not classified: TIP3:OH2 TIP3

o I patch termini with the patch residues ACE and CT3, leading to similar warnings like: iatmcls_286W> MODEL atom not classified: LEU:CAY LEU iatmcls_286W> MODEL atom not classified: LEU:CY LEU iatmcls_286W> MODEL atom not classified: LEU:OY LEU

For a HETATM residue that I added to the topology file no such warnings are produced.

Any hints on this?

Thanks a lot, Oliver