> I am trying to keep the 10 closest waters around a ligand in a DNA-ligand trajectory.
>
> The ptraj script I am using is:
> ------------------------------------------------------
> trajin md_reimaged.mdcrd 201 400
> trajout closest_waters.mdcrd
> strip :Na+
> closest 10 :13 oxygen
Looks fine if you want a trajectory that has just the solute, 10 waters
and box information (which requires a corresponding PDB or prmtop to view
appropriately).
Normally in this case I would add "nobox" to the trajout command to avoid
having box information.
> The output processing when the script is running looks like below:
...
> OUTPUT COORDINATE FILE
> File (closest_waters.mdcrd) is an AMBER trajectory (with box info)
...
> I have also tried noimage, closestwaters, different trajout filenames,
> not stripping the Na+ ions, and using varying number of trajin frames.
> However, this does not give a trajectory file I can view using VMD. I am
> able to view the original md_reimaged.mdcrd file and others like it but
> not this ptraj processed for closest waters. One strange thing that is
The key is how you view with VMD. You cannot load the original prmtop
file since this will have all the waters; there is no information in the
trajectory file to specify what atom is what, only a list of x, y, z for
atoms 1->N. Therefore you need some way to map and this requires either
loading a corresponding PDB file (with no ions and only 10 waters) or a
corresponding prmtop file (with no ions and only 10 waters).
--tec3
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Received on Fri May 04 2012 - 03:00:04 PDT
