Sorry for the delay on this.
Does the mol2 file have more or fewer atoms than the trajectory? If it
has more, you can strip off the excess and use that as a topology for
the trajectory. If it's the other way you could potentially generate a
"dummy" topology with the right number of atoms, but at some point
it's probably going to be important what those atoms are, so just
being able to get the coordinates will be of limited value. You really
will need to find some sort of information on what atoms are what
(either through CIF, PDB, Mol2, associated topology, whatever) moving
forward - otherwise the trajectory is just a series of not very
meaningful coordinates...
-Dan
On Mon, Mar 4, 2019 at 9:58 AM emanuele falbo <falbo.emanuele.gmail.com> wrote:
>
> 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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>
> --
>
> *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/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Mar 26 2019 - 12:30:03 PDT
