[gmx-users] H3 of NPRO missing in AMBER force field

Justin A. Lemkul jalemkul at vt.edu
Wed May 23 18:17:57 CEST 2012

On 5/23/12 4:08 PM, SebastianWaltz wrote:
> On 05/23/2012 02:16 PM, Justin A. Lemkul wrote:
>> On 5/23/12 12:17 PM, SebastianWaltz wrote:
>>> Hallo together,
>>> in the amino acid data base file (aminoacids.rtp) of the amber99sb-ildn
>>> force field the H3 hydrogen of NPRO is missing.
>>> Would be nice if someone could add the missing parameters or pose them.
>> There is no H3 in NPRO.  It is a secondary amine, so three H atoms
>> would give it five bonds.
>> -Justin
> As far as I remember the NPRO (like the NLEU) in the amber force field
> stands for the protonated N-termini of PRO and therefore should have
> three hydrogens like NLEU NALA and so on.

The "N" prefix simply means it is at the N-terminus, not necessarily that it is 
protonated, though the typical forms of the terminal amino acids bear a net 
charge in this group.

Back to the original question - have a look at the structure of proline; it is 
quite different from every other amino acid since it contains a secondary amine.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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