Hi Jose,
> I want to write a new action in ptraj that requires prior knowledge of
> the
> average coordinates. Is this possible in a single ptraj session? As I
> understand the code, the trajectory is read only once and all requested
> actions are performed on the current snapshot, as the "trajectory
> pointer"
> goes through the trajectory.
> Since my action needs the average coordinates *a priori*, I need to
> read the
> trajectory twice. Can this be done in a single ptraj session?
I believe that you would need to modify the code in order to support this as
you describe it. However, the easiest approach might be to simply require a
reference structure which your action uses and this reference structure is
'assumed' to be the average structure. One would then run ptraj to write a
pdb of the average structure and then you run ptraj again to read this pdb
file as the reference structure. This might be conceptually easier to
implement even if it is not quite as clean with regards to how one runs it.
This could be easily scripted though with a shell script calling both the
ptraj runs, or even writing the necessary input files if needed.
All the best
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
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Received on Mon May 24 2010 - 18:30:06 PDT
