Hi,
If you are not interested in computing, e. g., the diffusion coefficient, you can safely image the trajectory if basically you do not care about the distance traveled by the molecule.
You simply add the command "image" after you have loaded the trajectory.
Please check Amber manual, everything is well explained.
Tommaso
Inviato dal mio dispositivo mobile Huawei
-------- Messaggio originale --------
Oggetto: Re: [AMBER] Ris: Extracting PDBs every 'N" ns
Da: Jag Silwal
A: AMBER Mailing List
CC:
Hi Tommaso,
Could you please elaborate a little more on 'imaging trajectory' to extract
PDB at certain interval? How would I change my input that I had mentioned
in my previous email?
Thank you again.
Sincerely,
Jag
On Sun, Dec 2, 2018 at 10:45 AM Casalini Tommaso <
tommaso.casalini.chem.ethz.ch> wrote:
> Dear Jag,
> I would suggest to image your trajectory, so that you keep everything into
> your simulation box avoiding coordinates problem.
>
> Hope this helps!
>
> Tommaso
>
> Inviato dal mio dispositivo mobile Huawei
>
> -------- Messaggio originale --------
> Oggetto: [AMBER] Extracting PDBs every 'N" ns
> Da: Jag Silwal
> A: AMBER Mailing List
> CC:
>
> Dear all,
> I just ran a long simulation for a protein-protein interaction complex with
> following input for final production steps with dt=0.002,= ntpr=1000,
> ntwx=10000, ntwr=10000, for a total of 800 ns. After ~ 400 ns, there seems
> to be a drastic change of binding free energy at the interface and I would
> like to compare the structure of the complex before and and after 400 ns.
> Ideally, I would like to capture representative average PDB for every 20 ns
> (total 40 PDBs) and align them all to compare.
> I took Dan's suggestions from amber mailing list and tried this:
>
> 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"
>
> Could you please guide me to the right direction and suggest if I am doing
> something wrong here? How about if I want only two structures, one average
> before 400 ns and another averaging after 400 ns?
>
>
> I am kind of stuck in this last step of my analysis and I would greatly
> appreciate you help.
>
> Sincerely,
> Jag
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Received on Sun Dec 02 2018 - 08:30:02 PST
