Re: [AMBER] amino-cyclopropyl parameters

From: Loris Moretti <>
Date: Wed, 31 May 2017 07:32:48 +0000

Yes, of course. Here in attachment the pdb I've used, which is the minimal example for the case.

I see what you mean with the cx-cx-na and I've experienced another odd parameter of a similar kind, cx-cx-nh which leads to a wrong minimized structure.

I tested the transposition of values and I get reasonable results.



From: David A Case <>
Sent: Tuesday, May 30, 2017 3:52:05 PM
To: AMBER Mailing List
Cc: Junmei Wang
Subject: Re: [AMBER] amino-cyclopropyl parameters

On Tue, May 30, 2017, Loris Moretti wrote:
> In the gaff parameters file dat/leap/parm/gaff2.dat the line
> corresponding to the angle term I need is:
> cx-cx-n3 114.892 59.590 SOURCE4_SOURCE5 400 0.3281
> In the literature one can find that such angle should be around 114
> degrees. So, my guess is that the 2 values have been exchange by
> mistake, in fact once replaced the simulation went fine.

Thanks for reporting to Junmei for his input. Junmei:
Some of the cx-cx-XX entries look quite odd: e.g. compare cx-cx-n3 to
cx-cx-na. But I suspect this is more of an atom-typing glitch than a
transposition of values. It looks like antechamber is expecting cx-cx-n3
to be in a three-member ring, but that is not happening here (cf. pictures

Loris: can you post the pdb file you fed to antechamber? We'll try to
get to the bottom of this.


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Received on Wed May 31 2017 - 01:00:02 PDT
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