Dear Gustaf
Thank you for your kind reply.
I did following:-
trajout out_frame-500.pdb pdb multi nobox onlyframes 500,500,1
and get this message in cpptraj:-
Saving frames *1 500*
Writing 'out_frame-500.pdb' as PDB
The output file I assume contains both frames 1 and 500.
Should I use it without the keyword "multi"
Will it be the right option?
Also can I same rst file in a similar manner if I am not saving the PDB
file?
Regards
Sadaf
On Wed, 17 Mar 2021 at 18:49, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> I’m just guessing here, though the syntax from what I remember is start,
> stop, step
>
> Meaning you would want 500,500,1, 1500,1500,1 ….
>
>
> > trajout out_frame.pdb pdb multi nobox onlyframes 1,2000
>
> trajout out_frame-500.pdb pdb multi nobox onlyframes 500,500,1
> trajout out_frame-1500.pdb pdb multi nobox onlyframes 1500,1500,1
> trajout out_frame-2000.pdb pdb multi nobox onlyframes 2000,2000,1
>
> One PDB for each frame. You don’t need any rst file for a PDB.
>
> I am quite sure there are shorthands for “first” and “last” and
> potentially a better way to print each frame to a separate PDB. Though this
> should work and is as much as I could guess without looking in the manual.
>
> Best regards
> // Gustaf
>
>
> > On 17 Mar 2021, at 14:23, Sadaf Rani <sadafrani6.gmail.com> wrote:
> >
> > Dear Amber users
> > Please correct me on how should I save PDB and rst file at a specific
> > frame. I have a trajectory of 2000 frames and I want to save PDB files at
> > e.g first, 500, 1500, and 2000 frames.
> > I used the following command to save at first and 2000 frames however
> when
> > I load pdb in vmd it is loaded as a complete trajectory. Could anyone
> > please correct me?
> > I used the following command in cpptraj:-
> >
> > parm complex.prmtop
> > trajin Prod.nc
> > trajout out_frame.pdb pdb multi nobox onlyframes 1,2000
> >
> > Regards
> > Sadaf
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>
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Received on Wed Mar 17 2021 - 07:30:02 PDT
