On Sat, Apr 07, 2012, Jason Swails wrote:
>
> Leap adds hydrogens based on which hydrogens are present in the library
> file for that particular 3-letter codon. For instance, HIE and HIS are
> the same and are singly-protonated at the epsilon position. HID is
> singly-protonated at the delta position, and HIP is doubly-protonated.
Just a minor clarification: "HIS" is not defined in the underlying Amber
libraries. Most leaprc files have lines like this:
#
# assume that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE
This is where the default behavior for "HIS" is defined. If you want a
different default, modify those lines (probably in a copy).
....dac
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Received on Sat Apr 07 2012 - 14:00:03 PDT
