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

SebastianWaltz sebastian.waltz at physik.uni-freiburg.de
Wed May 23 16:08:18 CEST 2012

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.



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