Hydrogen problems with Modeller4
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 marsden@bioch.ox.ac.uk Home: +44 1865 552696 OCMS, Oxford Fax: +44 1865 275253 Work: +44 1865 275720 ---------------------------------------------------------------------
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. > > 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 marsden@bioch.ox.ac.uk Home: +44 1865 552696 > OCMS, Oxford Fax: +44 1865 275253 Work: +44 1865 275720 > ---------------------------------------------------------------------
-- 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 e-mail sali@rockvax.rockefeller.edu; http://salilab.org
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