Hi Dan,
Thanks for replying. I tried to upload the file.mol2 in vmd , and then
loaded the file.mdcrd (trajectory) as NetCDF file. However, the issue is
that it doesn't show any thing ( it says there is obviously a mismatch
between the number of atoms of the two files), and thus I can't save the
coordinate as xyz.
Also, I don't know have any clue whatsoever to re-generate the topology
files- all I have is the trajectory ( file.mdcrd and the file.out and the
restart file file.rst7)
So, I wonder if you could give me more info about retrieving it ?
Cheers,
Manuele
Il giorno lun 4 mar 2019 alle ore 13:54 Daniel Roe <daniel.r.roe.gmail.com>
ha scritto:
> Hi,
>
> You'll probably want to re-generate the topology at some point. That
> said, VMD (and cpptraj, which can also convert to .xyz format) can use
> a PDB/mol2 file (if you have one) as a topology file for the purposes
> of coordinate conversion.
>
> -Dan
>
> On Mon, Mar 4, 2019 at 5:09 AM emanuele falbo <falbo.emanuele.gmail.com>
> wrote:
> >
> > Dear admin and users,
> >
> > I'd like to save several snapshots into xyz files from the trajectory
> file.
> > Normally, I use vmd :
> > (i) load the topology " $ vmd file.prmtop" and (ii) from the editing
> window
> > I do open the trajectory file.
> >
> > However, by accident I deleted the original topology file used for the
> MD.
> > So, I wonder if there is any way I can use to retrieve the topology file,
> > or at least to save snapshots from the dynamics without it.
> >
> > Thanks in advance for the help.
> >
> > Cheers,
> > Manuele
> >
> >
> > --
> >
> > *Emanuele Falbo*
> > PhD student
> > Penfold group
> > School of Natural and Environmental Sciences
> > Bedson Building, Newcastle University
> > Newcastle upon Tyne, NE1 7RU
> > w: http://tompenfoldresearch.weebly.com/
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>
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--
*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
w: http://tompenfoldresearch.weebly.com/
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Received on Mon Mar 04 2019 - 07:00:02 PST
