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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