O3'-P (default) 1.60 , i got upto 4.6
could i correct it? on viewing through softwares other than leap those
bonds appear broken. any way to correct it. leap shows warning for 4.6, 3.4
and 3.7 bond distances. there are 2.5, 2.1, 1.5 etc bonds also for this
O3'- P distance but not included in warning.
On Wed, Sep 10, 2014 at 3:39 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> 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
>
>
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Received on Tue Sep 09 2014 - 20:00:02 PDT
