Alternatively, could be done with pytraj
import pyraj
traj = pytraj.load('your.nc', top='your.parm7')
for coords in traj.xyz:
# do something with coords
# e.g: follow this format:
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/xyz.html
# type coords: 2D array
Hai
On Mon, Jun 19, 2017 at 2:10 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> You could potentially use the 'ncdump' utility to extract the raw
> coordinates from the trajectory (i.e. ncdump -v coordinates <traj>)
> and post-process that output with something like awk.
>
> -Dan
>
> On Fri, Jun 16, 2017 at 11:19 AM, Shafaq Muzammal
> <Shafaq.Muzammal.nottingham.ac.uk> wrote:
> >
> > Hi,
> >
> >
> > Thanks, but i have to rewrite it into .xyz format and use it as input to
> some other software.
> >
> >
> > Kind Reagards,
> >
> >
> > Shafaq
> >
> > ________________________________
> > From: Elvis Martis <elvis.martis.bcp.edu.in>
> > Sent: Wednesday, June 14, 2017 10:39:34 AM
> > To: AMBER Mailing List
> > Subject: [Spam?] Re: [AMBER] convert .nc trajectories to .xyz
> >
> > Hi,
> >
> > I am not very but you can try VMD to export frames loaded as .nc to .xyz.
> >
> >
> > Best Regards
> >
> > [photo]
> >
> >
> >
> > Elvis Martis
> > Ph.D. Student (Computational Chemistry)
> > at Bombay College of Pharmacy
> >
> >
> > A Kalina, Santacruz [E], Mumbai 400098, INDIA
> > W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> > Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
> > [http://lnd.wisestamp.com/images/og-img.jpg]<https://
> webapp.wisestamp.com/#>
> >
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> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
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> >
> >
> >
> >
> >
> > ________________________________
> > From: Shafaq Muzammal <Shafaq.Muzammal.nottingham.ac.uk>
> > Sent: 14 June 2017 13:59:15
> > To: AMBER Mailing List
> > Subject: [AMBER] convert .nc trajectories to .xyz
> >
> > Dear All,
> >
> >
> > Does anybody know of a software or tool to convert the netcdf
> trajectories from AMBER to .xyz trajectory format?
> >
> >
> >
> > Kind Regards,
> >
> >
> > Shafaq
> >
> >
> >
> >
> > This message and any attachment are intended solely for the addressee
> > and may contain confidential information. If you have received this
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> >
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> > message or in any attachment. Any views or opinions expressed by the
> > author of this email do not necessarily reflect the views of the
> > University of Nottingham.
> >
> > This message has been checked for viruses but the contents of an
> > attachment may still contain software viruses which could damage your
> > computer system, you are advised to perform your own checks. Email
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> >
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> and related ...
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> >
> >
> >
> >
> >
> > This message and any attachment are intended solely for the addressee
> > and may contain confidential information. If you have received this
> > message in error, please send it back to me, and immediately delete it.
> >
> > Please do not use, copy or disclose the information contained in this
> > message or in any attachment. Any views or opinions expressed by the
> > author of this email do not necessarily reflect the views of the
> > University of Nottingham.
> >
> > This message has been checked for viruses but the contents of an
> > attachment may still contain software viruses which could damage your
> > computer system, you are advised to perform your own checks. Email
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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 Mon Jun 19 2017 - 12:30:03 PDT
