ok thank you sir.
On Wed, Sep 10, 2014 at 8:10 AM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > 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.
>
> ...this is an example of try it, and see what happens. As mentioned by
> DAC, minimization will try to adjust the bond into the correct range,
> however he notes that this may come at the expense of distorting other
> degrees of freedom. In general, when using significantly distorted
> structures, you have to worry that the large forces could overcome big
> barriers, for example, flips in chirality.
>
> First, try it. I would try minimization with generalized Born and then
> investigate the structure to make sure it is "reasonable" with your
> expectations. I would run my nucleic acid structure through Curves or
> some other analysis of nucleic acid structure to look for problems.
>
> Second, if distortions result, think of adding restraints to prevent
> unwanted transitions (in the dihedrals).
>
> If this still doesn't work, try to come up with a better way to generate
> the initial models...
>
> --tec3
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 09 2014 - 20:30:02 PDT
