Hello Amber user:
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:
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?
2. what's the meaning of the distance? It means the distance between the two correlated heavy atoms or the length of the hbond?
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?
_________________________________________________________________________________________________
Xiaoshu Xu
PhD candidate
Key Laboratory of Synthetic Biology
Shanghai Institute of Biological Sciences
Chinese Academy of Science(CAS)
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Received on Sat Feb 14 2015 - 23:30:02 PST
