Hi,
First, if imaging is a concern you should use 'autoimage' instead of
'center'/'image', or use the 'image' keyword of the 'hbond' command.
However, since it seems like you're only interested in intramolecular
hydrogen bonds the imaging is not necessary - in fact it's probably better
to strip the water prior entirely if you don't need it.
The 'lifetime' manual entry (section 29.11.12) contains an example of how
to perform lifetime analysis with hydrogen bond data. In your case you may
want something like:
hbond HB distance 3.5 angle 120 :1-6 out 3.5_nhb.dat avgout 3.5_avghb.dat
series
run
runanalysis lifetime HB[solutehb] out lifehb.dat
-Dan
On Wed, Jun 24, 2015 at 12:48 PM, Lara rajam <lara.4884.gmail.com> wrote:
> Dear Amber
>
> I tried calculating the hydrogen bond from cpptraj
>
> I am able to do the possible hydrogen bond between the solute residues 1-6
> as below
>
> trajin ../md1.mdcrd
>
> center :1-6
>
> image familiar
>
> hbond distance 3.5 angle 120.0 :1-6 out 3.5_nhb.dat avgout 3.5_avghb.dat
>
>
> but I am not able to do the life time for the same i tried as below
>
>
> trajin ../md1.mdcrd
>
> center :1-6
>
> image familiar
>
> hbond distance 3.5 angle 120.0 :1-6 out 3.5_nhb.dat avgout 3.5_avghb.dat
> series lifetime.data
>
>
> since the series word should be added with the following file name
>
>
> not able to get the out file ..
>
>
> let me know what error I am doing so that it can be fixed
>
>
> thank you
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jun 24 2015 - 13:30:02 PDT
