Hi,
You'll have to use the GitHub version of cpptraj:
https://github.com/Amber-MD/cpptraj
I recently introduced a bunch of enhancements and features for the
'hbond' command, one of which is the introduction of the
'bridgebyatom' keyword, which will give you the results you want. The
'hbond' command now also benefits from OpenMP (i.e. cpptraj.OMP,
cpptraj.OMP.MPI, etc). See
https://github.com/Amber-MD/cpptraj/pull/485 for full details.
Hope this helps,
-Dan
On Wed, Apr 26, 2017 at 10:27 AM, Joanna Sarzynska <asias.ibch.poznan.pl> wrote:
> Dear Amber users,
> I want to analyze a water bridge within the same residue.
> As I know, cpptraj was able to identify only the water bridge between
> two different residues. I have seen that currently hbond module in
> cpptraj is updated but still I can not figure out how to analyze the
> water bridge within the same molecule. I use CPPTRAJ: V16.16.
> Is there any version of cpptraj that can handle with intra-residue water
> bridge?
> Best,
> Joanna Sarzynska, Poznan
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Apr 26 2017 - 08:30:03 PDT
