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