> I have run dynamics on a certain protein PDB file with a given set of
> parameters. However, when I set up the parameters/PDB, I made a mistake:
> I mis-labeled two atoms in non-standard residues (I gave one the label
> C1 which should have been C3, vice versa). The dynamics are fine;
> however, my analysis software relies on correctly identifying C1 and C3
> in these non-standard residues.
>
> Is there a way to modify the atom labels after a trajectory has been run
> in the .mdcrd file? Currently, my solution is to generate a bunch of
> PDBs from the trajectory, edit them to switch the labels back, but this
> seems most inefficient.
The trajectory files only contain coordinates without atom labels. This
is why when doing analysis you need a "key" to match residue/atom names
to the coordinates. That key, in cpptraj, is a prmtop or psf or even a
PDB file.
--tec3
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Received on Fri Feb 19 2016 - 07:30:02 PST
