Re: [AMBER] distance restraint

From: Thomas Cheatham <>
Date: Tue, 9 Sep 2014 20:40:15 -0600 (MDT)

> 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...


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Received on Tue Sep 09 2014 - 20:00:02 PDT
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