[AMBER] angles and dihedrals for lone pairs

From: Ivanov, Maxim <maxim.ivanov.marquette.edu>
Date: Sun, 5 Aug 2012 23:39:47 +0000


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.

I would really appreciate if someone could give me a hint how I should proceed.

Thanks in advance,

Maxim Ivanov

Graduate Student
Marquette University
Chemistry Department
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Received on Sun Aug 05 2012 - 17:00:02 PDT
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