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How to avoid funny structure in all-hydrogen modeling?

Dear all,
Have anyone ever generated all-hydrogen models?
For all-hydrogen modeling, the generated models always have some funny 
structures(such as one hydrogen atom is connected with several other atoms. I 
think some maybe due to bad contact, but some bond lengths are longer than 
2.5 angstrom). These funny connections sometimes appear in ARG and SER. 
Is it possible because models have not been thoroughly refined? I have tried 
to set MODELLER "MD_LEVEL" to "refine_1" (# very thorough MD optimization), 
but no effects.
How to avoid or remove these funny structures in all-hydrogen modeling?
Thank you very much for your kind help! 
With best regards,
Kong Lesheng