Prof. David,
Thank you for your email. 'autoimage' seems to work for this.I just want to
check to make sure I am ding it right. So if I want to extract the PDB at
one particular time, lets say at 800 ns, can I just use the following
command then?
parm x.prmtop
trajin final.mdcrd
autoimage
outtraj snapshot1.pdb onlyframes 800000
and if I am saving frames every 20 ns for a total of 800 ns and want to
extract frames every 20 ns as PDB, I would use
parm x.prmtop
trajin final.mdcrd 20000 last 20000
trajout MyFrames.pdb multi
Am I doing it right?
Thank you again,
Sincerely,
Jag
On Sun, Dec 2, 2018 at 2:40 PM David Case <david.case.rutgers.edu> wrote:
> On Sun, Dec 02, 2018, Jag Silwal wrote:
>
> >
> >parm x.prmtop
> >trajin final.mdcrd 20000 last 400000
> >trajout MyFrames.pdb multi
> >
> >But got the following warning and only few frames are processed.
> >
> >"Warning: Coordinates are too large to fit in PDB format. Consider another
> >format.
> > 0% Warning: Coordinates are too large to fit in PDB format. Consider
> >another format.
> >100% Complete"
>
> Try inserting an "autoimage" command before the trajout command.
> Depending on your needs, you may also wish to carry out an rms command
> of the protein to (say) the coordinates at the first frame.
>
> No guarantees, but these commands are likely to bring the coordinates
> back into the range of the PDB format.
>
> ...dac
>
>
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Received on Mon Dec 03 2018 - 02:30:03 PST
