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.