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 - 08:00:03 PST
