Re: [AMBER] Calculating residence times with cpptraj

From: Daniel Roe <>
Date: Wed, 26 Sep 2018 15:08:57 -0400

Yes. What you could do is substitute :Na+ for
solventdonor/solventacceptor in the 'hbond' command (this will
automatically disable the angle criterion btw), and specify .OP? as
your mask for hbond. Make sure you use the series keyword so that the
time series data is recorded. Then you can use 'lifetime' analysis
just like you would for "normal" hbond output.

On Wed, Sep 26, 2018 at 12:55 AM Stefan Ivanov <> wrote:
> Dear Amber users,
> I am interested in calculating residence time series with cpptraj. I see Amber has a useful built-in function (lifetime), but the examples in the manual focus on HBond analysis. I need something more general. For example, is it possible to perform lifetime analysis on the residence times of Na+ within 5 angstrom of OP1 and OP2 of a nucleic acid?
> Thanks in advance.
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Received on Wed Sep 26 2018 - 12:30:02 PDT
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