Such that I could edit the prmtop file for this purpose?
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
> On Feb 19, 2016, at 10:01 AM, Thomas Cheatham <tec3.utah.edu> wrote:
>
>
>> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 19 2016 - 07:30:04 PST
