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[modeller_usage] Problems with stereo-chemical fixing of Hydrogen atoms



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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