do all pdb files have the same number of atoms? If yes, you can use pytraj
import pytraj as pt
pdb_files = [ ... ] # put a list of files here e.g: pdb_files = ['my0.pdb',
'my1.pdb']
traj = pt.iterload(pdb_files, top=pdb_files[0])
traj.save('new.nc')
# you can use python's glob
# from glob import glob
# pdb_files = glob('*.pdb')
Hai
On Fri, Nov 18, 2016 at 3:11 PM, Dmitry Suplatov <genesup.gmail.com> wrote:
> Dear Amber Users,
>
> can you suggest a plausible approach to converting a collection of PDB
> files (some 10 000 - 20 000 frames) to a NetCDF trajectory format? Input:
> PDB files; Output: .nc trajectory
>
> Thank you.
> Best,
> Dmitry
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Received on Fri Nov 18 2016 - 12:30:04 PST
