Re: [AMBER] cpptraj mask for hbond analysis

From: Daniel Roe <>
Date: Fri, 30 Mar 2018 15:00:15 -0400

On Fri, Mar 30, 2018 at 12:09 PM, Michael Yonkunas
<> wrote:
> hbond UUpair :6-15,36-46,O2,O4,H3 out nhb.dat avgout 6_all_avghb.dat series

This mask is likely not what you want. Assuming that O2 etc are atom
names and 6-15 are residue numbers, you want:


See 28.2.2. Atom Mask Selection Syntax in the cpptraj section of the
Amber 17 manual for details on mask selection. It can be helpful to
use the 'select' or 'atom' commands to test if the mask expression you
are using is behaving as intended. Also, setting the debug level to 1
(via debug 1) prior to the hbond command will print lists of donor and
acceptor sites, which may be useful as a debugging tool.

> I also noted that when masking atoms, neither the . nor the "." Are recognized.

Note that a period is not a valid operator for Amber mask syntax.
Please refer to the manual for details.

Hope this helps,


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Fri Mar 30 2018 - 12:30:04 PDT
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