Ravi Rathore wrote: > Q: Is it possible to built short-contact-free models (hydrogens > included) with Modeller? > > The models do have hydrogen atoms, however, I noticed that most of the > hydrogens have > short-contacts within the same atom or residue OR with neighboring > residues and also have long-range clashes.
Your input files look OK (and similar to the canonical example, in examples/all-hydrogens/ in the Modeller distribution).
> Assuming that there is everything fine with topology or parameter > files, I wonder, the energy minimization/MD should have corrected such > clashes.
Not necessarily. The main restraints used in optimization are homology-derived (which don't apply to hydrogens anyway) and van der Waals (which are small or nonexistent for hydrogens). Maybe you're thinking of electrostatics? Modeller doesn't use electrostatics by default, so you'd have to turn that on with SET DYNAMIC_COULOMB = on
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage