[AMBER] pyramidal amide nitrogen

From: Arnaud Bondon <arnaud.bondon.univ-rennes1.fr>
Date: Thu, 2 Apr 2020 20:17:38 +0200

Hi,

I use amber17 for solving peptide or pseudo-peptide structure using NMR
restraints.
I use antechamber when required for pseudo-peptides with gaff
Starting from structures .mol2 or .pdb generated with sirius or yasara

When looking at the structure after minimization (no NMR restraints)
some of the amide nitrogen display a pyramidal character.

However, the N sp2 is valid.

No ideas, help is very wellcome

arnaud

-- 
POUR UNE RECONNAISSANCE DE LA PALESTINE DANS LES FRONTIERES DE 1967
OU UN ETAT COMMUN
Arnaud BONDON
Equipe CORINT, UMR CNRS 6226
PRISM
CS 34317
Campus de villejean
Université de Rennes 1
35043 RENNES Cedex France
tel: (0)2 23 23 65 61
arnaud.bondon.univ-rennes1.fr
http://iscr.univ-rennes1.fr
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Received on Thu Apr 02 2020 - 11:30:02 PDT