[modeller_usage] HSE problem solved, new question

[Oliver Hucke <>]

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

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Oliver Hucke (PostDoc)
Biomolecular Structure Center
Dept. of Biochemistry
University of Washington
Health Sciences Building K-418C
1959 NE Pacific St
Seattle, WA 98195
T:(206)685-7046
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