Re: [AMBER] question on protonation state of histidine

From: case <>
Date: Sat, 7 Apr 2012 16:42:18 -0400

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

This is where the default behavior for "HIS" is defined. If you want a
different default, modify those lines (probably in a copy).


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Received on Sat Apr 07 2012 - 14:00:03 PDT
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