Re: [AMBER] hbond lifetime cpptraj

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 24 Jun 2015 15:00:06 -0600

Hi

On Wed, Jun 24, 2015 at 2:32 PM, Lara rajam <lara.4884.gmail.com> wrote:

>
> hbond MyHB :1-6 out try.dat dist 3.5 angle 120 avgout tryavghb.dat
> nointramol series solventacceptor :WAT.O solvent donor :WAT solvout
> sovent_avg.dat bridgeout bridge.data
>

:WAT.O is not a valid mask. You probably want :WAT.O, (@ is the character
for "atom"). I recommend reviewing section 29.1.6 on atom mask selection
syntax.

-Dan


>
>
> run
>
> writedata solutehb.dat MyHB[solutehb]
>
> writedata solventhb.dat MyHB[solventhb]
>
> lifetime MyHB[solutehb] out solute.lifetime.dat
>
> lifetime MyHB[solventhb] out solvent.lifetime.dat
>
> runanalysis
>
>
>
> the script is not working I made mistake on defining the water donor or
> acceptor molecules
>
> could any one help me to fix this
>
>
> thank you
>
> On Wed, Jun 24, 2015 at 2:48 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
> >
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>



-- 
-------------------------
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 - 14:30:03 PDT
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