Dear Amber
Could you please fix me with the correct command:-
I want to save the 2000th frame from the trajectory, so the start,stop and
step is 2000.
When I use command:-
trajout outframe-2000.pdb pdb nobox onlyframes 2000,2000,2000
I get :-
OUTPUT TRAJECTORIES (5 total):
'outframe-2000.pdb' (2000 frames) is a PDB file no box info,: Writing
frames 2000
(2000 frames) are being processed only and only 2000th no is written in pdb
file or otherwise. Could you please remove my confusion?
Regards
sadaf
On Wed, 17 Mar 2021 at 19:09, Sadaf Rani <sadafrani6.gmail.com> wrote:
> 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
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Mar 18 2021 - 01:00:02 PDT
