use distance command to output distance between a point on your ligand and
a point on your protein. this should output a file with frame number and
distance columns.
write a script (e.g. python) that selects the frames that have a distance
under 15 A. then feed this into ptraj so it writes out a new co-ordinate
file with only those frames.
not sure what you meant by the pdb bit at the end of your message. did you
mean crd?
cheers,
ET
On 14 March 2012 01:27, <tdo.chem.ucsb.edu> wrote:
> Hello,
>
> I try to use ptraj/cpptraj to sort my trajectory based on the
> protein-ligand distance. I want to remove all of the snapshots in which
> the distance between protein and ligand is greater than 15 angstroms and
> store the rest of the trajectory into one PDB. Please give me some
> suggestions.
>
> Thanks,
>
>
>
>
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Received on Wed Mar 14 2012 - 12:00:02 PDT
