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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