Hydrogen problems with Modeller4

Brian Marsden marsden at bioch.ox.ac.uk
Tue Dec 30 11:32:33 EST 1997


I'm having a bit of a torrid time trying to get Modeller4 to cope with
hydrogens. Here's the scenario:

I have a template pdb file (directly from the Brookhaven PDB databank)
which contains an NMR structure and therefore contains all hydrogens.
Looking at the FAQ in Modeller's documentation I find that I probably
need to add the following lines to get-model.top:

SET HYDROGEN_IO=on  
SET TOPOLOGY_MODEL=1
SET TOPLIB = '${LIB}/top.lib'
SET PARLIB = '${LIB}/par.lib'

I then run Modeller in the usual way and end up with models with a huge
number of violations, and whopping great big gaps in the backbone. 

Strangely, if I strip the pdb file of all its hydrogens, remove the SET
HYDROGEN_IO=on and put TOPOLOGY_MODEL to 3 everything is fine - a nice
model is made, but, of course, without any hydrogens.

I'm probably doing something daft - can anyone out there point me in the
direction?

Many thanks.

Brian.

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