On Tue, Sep 06, 2011, George A. Khoury wrote:
> Upon looking at the structure, I noticed that my N-terminus has only 1
> hydrogen instead of the usual 3. It is my understanding that in the natural
> amino acids a residue at the N-terminus (i.e. Ala) will be replaced by a
> NAla, which will have the proper valence for the N-terminus.
The reason that this happens for natural amino acids is that Amber has
pre-calculated residues (called NALA, etc.), and a procedure for automatically
using those for the first residue of a chain (see the standard leaprc files).
If you want an NH3+ group for you non-standard aa, you will have to build such
a residue yourself. As Francois pointed out, R.E.D. offers one way to do
this.
....dac
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Received on Wed Sep 07 2011 - 13:00:02 PDT
