Re: [AMBER] angles and dihedrals for lone pairs

From: Ivanov, Maxim <>
Date: Tue, 7 Aug 2012 22:19:48 +0000

Thank you Dr. Case for your reply.

I looked at the code in extra_pts.f and played a little bit with TIP5P water and got confusedů
According to the code EP around oxygen in TIP5P has to be in tetrahedral sites with angle between two EP equal 54.735*2=109.470. And this angle has to be fixed.
However, minimization of TIP5P give values around 109.5 degrees depending on number of steps. What is the reason for this?
As I understand, it can't be because of energy minimization since EP don't have any forcefield parameters except bond length. By the way, bond length is varying in the forth decimal place as well which also confuses me since I set the value to 0.7000 in frcmod file. It is too large error to be computational error, there must be something behind.

Also, in parm99EP.dat I can see that there are some values for angles between atoms and EP (like EP-S-EP). Do they play any role in calculations at all?

Thank you,

Maxim Ivanov

On Aug 6, 2012, at 8:06 AM, case wrote:

> 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 Tue Aug 07 2012 - 15:30:04 PDT
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