> Yep, generally I remove all hydrogen before using leap...just logically
> it's a bit controversial that leap can't process files produced by Amber
> without any modifications.
If extra atoms were ignored, this could lead to silent problems
with pdb's of other origin. Maybe it wouldn't be too bad to ignore
extra H's, although it could lead to undetected chirality flips if
the ignored/misnamed H were in nonstandard chirality (I guess this
happens anyway if one just strips H's from input pdb).
Bill
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Received on Thu Jun 10 2010 - 10:00:05 PDT
