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
information.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 09 2014 - 15:30:03 PDT
