Re: [AMBER] angles and dihedrals for lone pairs

From: case <>
Date: Mon, 6 Aug 2012 09:06:17 -0400

On Sun, Aug 05, 2012, Ivanov, Maxim wrote:
> I want to do molecular dynamics of S-nitrosated cysteine and I
> want my -SNO residue to have two lone pairs at sulfur out of -SNO
> plane. However, when I am preparing files for my system using xleap, it
> doesn't ask me to include angles and dihedrals in frcmod file, it ask
> only for bond parameters of S-EP. And so minimization works fine without
> specifying angles and dihedrals. The only thing I can think about is
> that those parameters are hardcoded somehow, but for my project I need
> to vary those parameters.

> I looked at the define_frames() in extra_pts.f and found that it
> specifies some value for some angle, but I am not sure if I am going in
> the right direction.

You are going in the right direction. If you want to define your own extra
points, you have to grok the code in extra_pts.f. It sounds like you want
some variant of the TIP5P parameters.

It is also correct that you need only the "bond length" S-EP parameters: the
angles are determined by the type of extra point. The code tries to
automagically determine the type, but you should add a print statement to make
sure you are getting what you expect. You could also just visualize the
structure with the EP atoms present.

....good luck....dac

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Received on Mon Aug 06 2012 - 07:00:03 PDT
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