On Thu, Nov 23, 2006, Jordi Rodrigo De Losada wrote:
>
> I'm planning to obtain some snapshots(in PDB format) from a dynamics. In
> the previous versions of Amber I used the CARNAL module in order to get
> these pdbs. I've tried to find in the manual how to get this snapshots
> using ptraj. I saw that I can get an average of my dynamics and also
> analyze the results, however, I didn't find how to obtain some snapshots.
> For instance, if I run a dynamics of 250 ps and I want to recover a pdb
> file every 10 ps (so 25 pdbs at the end) what command or module should I
> use?
Something like this:
trajin <filename> 10 250 10
trajout <pdb-filename> pdb
The first line takes every 10th snapshot (starting from number 10, ending at
number 250). If your trajectory has a snapshot every picosecond, this would
do what you want. If your trajectory has a different time interval, modify
accordingly.
The second line saves the snapshots in PDB format.
...dac
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Received on Sun Nov 26 2006 - 06:07:15 PST
