Hi Robert,
For the purposes of making the analysis program work, just switching the respective C1 and C3 occurrences in the prmtop file should do the trick.
—
Gustavo Seabra.
> Em 19 de fev de 2016, à(s) 11:54, Robert Molt <rwmolt07.gmail.com> escreveu:
>
> Good morning,
>
> 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.
>
> --
> Dr. Robert Molt Jr.
> r.molt.chemical.physics.gmail.com
>
>
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Received on Fri Feb 19 2016 - 10:00:03 PST
