Re: Hydrogen problems with Modeller4
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 > azat@salilab.org, 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) martin@biochem.ucl.ac.uk (Home) andrew@stagleys.demon.co.uk URL: http://www.biochem.ucl.ac.uk/~martin Tel: (Work) +44(0)171 419 3890 (Home) +44(0)1372 275775
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 > > azat@salilab.org, 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) martin@biochem.ucl.ac.uk (Home) andrew@stagleys.demon.co.uk > URL: http://www.biochem.ucl.ac.uk/~martin > Tel: (Work) +44(0)171 419 3890 (Home) +44(0)1372 275775
-- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat@salilab.org - WWW/URL: http://salilab.org/~azat
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Azat Badretdinov