Dear modellers,
Q: Is it possible to built short-contact-free models (hydrogens included) with Modeller?
I am building an all-atom model using following scripts,
In modeller 7v7: SET TOPOLOGY_MODEL = 1, HYDROGEN_IO = on SET TOPLIB = $(LIB)/top_allh.lib SET PARLIB = $(LIB)/par.lib CALL ROUTINE = 'model' -----------------------------------------
In modeller6:
SET TOPOLOGY_MODEL = 1, HYDROGEN_IO = on SET TOPLIB = $(LIB)/top.lib (also tried top_allh.lib) SET PARLIB = $(LIB)/par.lib CALL ROUTINE = 'model' -------------------------------------------
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. Assuming that there is everything fine with topology or parameter files, I wonder, the energy minimization/MD should have corrected such clashes.
Then, I tried to use other, thorough optimization protocols, but of no use:
SET LIBRARY_SCHEDULE = 1 SET MAX_VAR_ITERATIONS = 300 SET MD_LEVEL = 'refine_5' SET REPEAT_OPTIMIZATION = 3 SET MAX_MOLPDF = 1E6
I would be grateful for any suggestion on proper stereo-chemical fixing of hydrogen atoms with Modeller.
Sincerely, Rathore, R.S.
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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
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Modeller Caretaker -
Ravi Rathore