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Re: Hydrogen problems with Modeller4



What you did should work. Can you please email the input files to
, so that Azat can take a closer look.

Thanks, Andrej


Brian Marsden wrote:
> 
> 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.
> 
> ---------------------------------------------------------------------
>  Brian Marsden           Home: +44 1865 552696
>  OCMS, Oxford     Fax: +44 1865 275253         Work: +44 1865 275720
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--
Andrej Sali, Assistant Professor
The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540
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