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 - 08:00:04 PST
