Re: Parametarization and geometry optimization. .

From: Ajasja Ljubetič (
Date: Tue Nov 20 2012 - 08:25:34 CST

Well if this bending is just the result of the flexibility of torsional
angles, then there should be no problems...

Best regards,

On 20 November 2012 15:14, Martin, Erik W <> wrote:

> Its hard to say without seeing some specifics like how much the "bent" and
> "extended" structures actually vary. However, I'd be inclined to say no,
> you shouldn't do this. Even if in a vacuum the energy minimized state of
> the cofactor is extended this does not mean it will remain that way in a
> protein environment. The CS coordinates might be perfectly accurate. My
> suggestion would be to rerun the Gaussian calculation. This time, fix
> heavy atoms that are well resolved in the CS and let the rest of the
> cofactor minimize.
> -Erik
> ________________________________________
> From: [] On Behalf Of
> Dhiraj Srivastava []
> Sent: Tuesday, November 20, 2012 7:26 AM
> To:
> Subject: namd-l: Parametarization and geometry optimization. .
> Hi
> I am trying to develop Charmm parameter for my cofactor. While doing
> geometry optimization by Gaussian, the Cofactor is going from the bend
> conformation (from Crystal structure) to extended conformation. Now my
> question is, the cofactor in my protein is in bend conformation and the
> parameter I am developing is for extanded conformation, So is it ok to use
> the parameter for extended conformation into my simulation?
> Thank you
> Dhiraj
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