Re: [AMBER] problem after minimization of pure DMF

From: David A Case <>
Date: Mon, 28 Oct 2013 07:44:36 -0400

On Mon, Oct 28, 2013, Sohag Biswas wrote:

> I'm trying to minimize the initial structure 50 DMF. After minimization, i
> can see that my methyl hydrogens of DMF are making bond.

Can you say exactly how you "saw" that methyl hydrogens were making a bond?
Visualization programs often are rather arbitrary in deciding where to draw
bonds. The bonds actually used in molecular mechanics are fixed: they can
neither be made nor broken by minimization.

Also, it's unclear how you created the parameters and topology for your file.
Or, what you mean by "50 DMF". If you are getting back geometries, there can
be many reasons, and these cannot be debugged remotely without more


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Received on Mon Oct 28 2013 - 05:00:03 PDT
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