Thanks for the suggestion, however I still have problems
(I am trying to educate my self on cpptraj, I mainly used some basic ptraj commands before):
I want to read mdcrd and mdvel files, find the closest solvents and printout the stripped mdcrd and mdvel files
(or a combined file).
I tired the following (testing with two frames):
parm Acet_meoh.prmtop
trajin mdcrd mdvel 1 2 1
trajout mdcrd
solvent byres :MOH
closest 8 :MOL.C1,C2 oxygen closestout closest_meohtest.dat outprefix closesttest
go
There is no message that velocity files are read and no velocity information in the output so above does not work,
hence my question is if it is possible to read both mdcrd and mdvel files (or transform them to a NetCDF format)?
Kind regards,
Pär
________________________________________
Från: Daniel Roe <daniel.r.roe.gmail.com>
Skickat: den 24 augusti 2017 23:00
Till: AMBER Mailing List
Ämne: Re: [AMBER] Closest velocities
If the velocities are present in the input trajectory they should be
present in any output trajectory when 'closest' is used. So you can
just use 'trajout' to write an output trajectory.
-Dan
On Thu, Aug 24, 2017 at 3:20 PM, Pär Håkansson <Nils.Hakansson.oulu.fi> wrote:
> Dear Amber list,
>
>
> Using AmberToos16, I have extracted the eight closest solvent molecules to my s?olute "MOL"
>
> with the following line in cpptraj script:
>
>
>>closest 8 :MOL.C1,C2 oxygen closestout closest_meoh.dat outprefix closest
>
>
> providing a striped set of coordinates of MOL+8solvents.
>
>
> I have solvent index for each timestep in "closest_meoh.dat", and I could
>
> write my own program/script. However,
>
> my question is if there is any route to use cpptraj (or other available tools)
>
> to extract the corresponding velocities?
>
>
> Kind regards,
>
> Pär
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Tue Aug 29 2017 - 01:00:02 PDT
