[AMBER] cpptraj mask for hbond analysis

From: Michael Yonkunas <m.yonkunas.usciences.edu>
Date: Fri, 30 Mar 2018 16:09:27 +0000

Dear All,

I am using the following cpptraj script (AmberTools16) to do a hydrogen bonding analysis of an RNA. The RNA is in a helical conformation but is a single strand 5' to 3'.

parm ../mth_disrupted_nowat_noion.prmtop
trajin mth_disrupted_nowater_noions_last250ns.nc
hbond UUpair :6-15,36-46,O2,O4,H3 out nhb.dat avgout 6_all_avghb.dat series
lifetime UUpair[solutehb] out all_pair.lifetime.dat

What I see from simulation (via VMD) for example is base pairing across the helix (8-45, 12-39, etc.).

Everything works fine with the exception of the mask. It is picking up atoms named O2', O4' etc. as they exist in the sugar ring. I tried various iteration of masking (i.e.: :6-15,36-46,O2,O4,H3&!(?'), as well as simply :6-15,36-46,O2,O4,H3&!(O2'). I also noted that when masking atoms, neither the . nor the "." Are recognized. It is only when I include the atom names as part of the list do they get parsed.

In addition, looking over the output that works as stated above I see intramolecular hbonds as well (8-8, 45-45, etc.) as is to be expected. Although when I include the "nointermol" flag the output, while completed, shows no hbonds at all.

I have not come across such behavior before, have been using Amber for a while. Any insight would be much appreciated.

Michael Yonkunas Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
University of the Sciences | https://www.usciences.edu/
Baird-Lab | https://sites.google.com/usciences.edu/bairdlab

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Received on Fri Mar 30 2018 - 09:30:02 PDT
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