Sorry, the RST file.
I don’t have enough information to know why you desire a RST file with a PDB file but still.
trajout filename.rst7 restart
The restart format seems to not have that many options so here my first suggestion would be
trajin somefile
trajout filename.rst7 restart 500 500 1
trajout filename.rst7 restart 1500 1500 1
trajout filename.rst7 restart 2000 2000 1
I am pretty sure there are other tools available in cpptraj for generating restart files, likely with more options, though at the moment I am drawing a blank. Something with coords/crd or similar.
// Gustaf
> On 18 Mar 2021, at 09:39, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> So, now looking at the manual. As usual there are numerous ways to achieve the same goal. I have not tested any of the suggestions so you need to consult the manual and edit as needed.
>
> I am assuming you are looking for a single PDB file per frame and not a multimodal PDB file with all three frames in one file. In that case, select a method using “multi” but replace multi with model, or just remove multi as model is the default.
>
> You can read in only the frames you are looking for defining only to read the three frames in question, then you can use “multi” to dump every frame as a separate pdb file. Then you do not need start/stop/step or onlyframes
>
> trajin somefile 500 500 1
> trajin somefile 1500 1500 1
> trajin somefile 2000 2000 1
> trajout output-filename pdb nobox multi
>
> You can use the onlyframes and specify a range
>
> trajin somefile
> trajout output-filename pdb onlyframes 500,1500,2000 multi
>
> This should create 3 PDB files with frame numbers added to the filename. Finally, just write every desired single frame as a PDB file
>
> trajin somefile
> trajout output-filename-500 pdb nobox 500 500 1
> trajout output-filename-1500 pdb nobox 1500 1500 1
> trajout output-filename-2000 pdb nobox 2000 2000 1
>
> These are the interesting sections of the manual
>
> 32.3.3. Ranges
> 32.10.4. trajin
> 32.10.5. trajout
> 32.10.5.1. Options for pdb format
>
> Best regards
> // Gustaf
>
>> On 17 Mar 2021, at 15:09, 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
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Received on Thu Mar 18 2021 - 02:30:02 PDT
