Re: [AMBER] atom type for N bond to conjugated chain using antechamber

From: Karl N. Kirschner <>
Date: Fri, 5 Jul 2013 09:34:28 +0200 (CEST)

Hi Zhonghe,

  The structure diagrammed in your email is unclear to me, with the format/font being altered and with no color. I think I have figured it out as R1-N(-R2)-C(=N)-N-C(=N)-N, and well answer based on this.

  For me, it is unclear which gaff atom type should be assigned to each of the nitrogen atoms. Did you check the resulting frcmod file to see how many parameters require attention with the atom types that antechamber assigned?

  It has a somewhat similar composition as an arginine. Depending on the pKa of this molecule it could be protonated. Then by analogy, the outer atom types would become N2, as defined by the protein force field. I might even assign N2 to the inner nitrogens as well, and see how many missing parameters then result.

  Ultimately, if you want to have confidence that your final parameters (as defined by your atom types and connectivity) are reliable/trustworthy, you would need to compare the molecular mechanics torsion curves of an analogue that contain this chemical functionality to quantum mechanics target curves. The Wolf2Pack (W2P) website would enable you to do this. Currently I do not have a molecule that contains your functionality and would have to generate the QM data for it. If you are interested in pursuing this route, let me know (e.g. via W2P's Message Board) and I will see what I can do.


----- Original Message -----
From: "zhonghe xu" <>
Sent: Friday, July 5, 2013 5:32:11 AM
Subject: [AMBER] atom type for N bond to conjugated chain using antechamber

 Hi all:
I prepare biguanide ligand for MD using antechamber with a command "antechamber -i xx.pdb -fi pdb -o xx.mol2 -fo mol2 -c bcc".
I have a question about atom type for N(highlighted in red) on conjugated chain, which were assigned to nh(N connected to aromatic ring in gaff). However, there is no aromatic ring(even a ring ) in molecular structure or file generated by antechamber.I wonder whether it is needed to modification or correction for this atomtype ? Thank in advance !
Best regard

  R2 N N
   | || |
 R1-- N --C--N==C--N

zhonghe xu

AMBER mailing list

AMBER mailing list
Received on Fri Jul 05 2013 - 01:00:02 PDT
Custom Search