Re: [AMBER] no parameter for nicotine

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 4 Feb 2015 05:12:23 -0500

> On Feb 4, 2015, at 5:07 AM, Harmeet Kaur <meet.academia.gmail.com> wrote:
>
> Dear Amber users,
>
> I could not save parameter file because my system has nicotine in it.
> Kindly suggest how to go about it. Fyi, I am using Amber 14.

Work through tutorial B4 (http://ambermd.org/tutorials/basic/tutorial4b/ <http://ambermd.org/tutorials/basic/tutorial4b/>) to learn how to use gaff to parametrize a non-standard residue. [1] Then apply that workflow to nicotine.

HTH,
Jason

[1] A ‘standard’ residue is one of the 20 common amino acids or 8 common nucleotides. 

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 04 2015 - 02:30:04 PST
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