On Fri, Dec 02, 2022, Kari Gaalswyk via AMBER wrote:
>
>I am trying to generate a .top file from a single snapshot of a CAMPARI
>trajectory (.pdb that has gone through pdb4amber) for clustering with
>cpptraj. However, tleaps' automatic atom reordering results in a top
>file that no longer matches the trajectory. I want to avoid loading each
>individual frame (as there are 27,000 frames) into tleap, however I can't
>find a way to prevent this reordering. I also cannot make use of cpptraj's
>atommap or parmed's addPDB without a .top that matches the trajectory
>ordering and CAMPARI doesn't output a topology (only a Z-matrix file in
>Tinker format). Is there a way to get tleap to adhere to the atom ordering
>in the pdb, or better yet, a way to reorder the trajectory to match the new
>top file?
You don't say exactly what "automatic atom reordering" means. The ordering
of atoms within a residue is determined by the libraries that get loaded.
You could create your own libraries with the CAMPARI ordering (if this is
indeed the problem), but that would also be a lot of work.
If you can convert one snapshot to pdb format, are you sure it is not simplest
to write a script to do that 27000 times? Then load those into cpptraj and
convert back to an Amber-compatible trajectory format like netCDF? Computers
are good at doing boring repetitive tasks.
...good luck...dac
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Received on Fri Dec 02 2022 - 14:00:02 PST
