Hi,
On Sun, Feb 15, 2015 at 12:06 AM, 徐晓庶 <xsxu.sibs.ac.cn> wrote:
> I have some questions about the analysis of hbond by Ptraj. My code was " hbond distance out 3.5 angle 120.0 donor acceptor", and the results of distance seemed ok, as all the distances were about 2.8 Å". However, the resulting angles are between 20° to 50°, were they right? From the results, I have the following questions:
Ptraj reports hydrogen bond angles as deviation from linear (180 deg),
so the actual angles are 180 minus those numbers.
> 1. The cutoff of angles was 120, was it mean that the angles less than 120° would be calculated? If I'm right, how about the linear hbonds? Would they will be neglected?
No, angles greater than 120 (closer to linear) will be calculated.
> 2. what's the meaning of the distance? It means the distance between the two correlated heavy atoms or the length of the hbond?
The average distance between the donor and acceptor (i.e. heavy) atoms
when the hydrogen bond is present.
> 3. How do you think about the strength of hbonds? In my opion, it will be affected by the length and the angle. What're the optimal angles of the hbonds?
There is no explicit hydrogen bond term in the force field, so
hydrogen bond "strength" comes only from the non-bonded terms (which
are distance-dependent only). The angle cutoff is just a way of
weeding out geometries that one would typically not consider hydrogen
bonded. From this analysis you can really only say how often a
hydrogen bond is present, but that says nothing about the actual
strength of the interaction.
Hope this helps,
-Dan
>
> _________________________________________________________________________________________________
>
> Xiaoshu Xu
>
> PhD candidate
>
> Key Laboratory of Synthetic Biology
>
> Shanghai Institute of Biological Sciences
>
> Chinese Academy of Science(CAS)
>
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>
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--
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
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Received on Sun Feb 15 2015 - 09:00:02 PST
