Re: Hydrogen problems with Modeller4

[Azat Badretdinov <azat>]

Dear Andrew and Brian!

please replace BUILD_MODEL INITIALIZE_XYZ = off
to  BUILD_MODEL INITIALIZE_XYZ = off, BUILD_METHOD =
'INTERNAL_COORDINATES'

in file $MODINSTALL/scripts/__generate_model.top

and 
SET TOPLIB = '${LIB}/top_allh.lib'
in your .top file.

Happy landings!

Yours,

Azat

Andrew Martin wrote:
> 
> 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.
> > >
> 
> ----------------------------------------------------------------------------
> Dr. Andrew C.R. Martin                             University College London
> EMAIL: (Work)     (Home) 
> URL:   http://www.biochem.ucl.ac.uk/~martin
> Tel:   (Work) +44(0)171 419 3890                    (Home) +44(0)1372 275775

--
- Dr. Azat Badretdinov 
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