Re: [AMBER] distance restraint

From: David A Case <>
Date: Tue, 9 Sep 2014 18:09:39 -0400

On Wed, Sep 10, 2014, Mary Varughese wrote:
> I have some incorrect (long) O3'-P bonds in the backbone of a nucleic acid
> structure. Overall the structure has some problems but i would like to
> focus first on backbone. Could i do a distance restrained minimization to
> correct this.? i dont know this method.
> Or could a general minimization procedure correct this?

Any sort of molecular mechanics minimization can fix such a problem. But
you need to think about how long the incorrect bonds are: if they are more
than a few tenths of Angstrom too long, then minimization may introduce
other problems in the structure. It's hard to be helpful without more


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Received on Tue Sep 09 2014 - 15:30:03 PDT
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