I have had very similar problems with Modeller4: huge numbers of
violations and gaps in the backbone even without hydrogens. However,
my .top files (generated by my MINT program) contain the command
SET HYDROGEN_IO=off
I haven't had time to analyse exactly what's going on yet (for the
moment I've gone back to Modeller3). I'll try to take another look
in the next few days.
I too have assumed I've been doing something stupid and have just
downloaded Modeller4 again to try installing from scratch again.
Andrew
> 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.
> >
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Dr. Andrew C.R. Martin University College London
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URL: http://www.biochem.ucl.ac.uk/~martin
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