search

openmm / openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.
1.49k stars 521 forks source link

No such file or directory: 't4-lysozyme-L99A-with-benzene.pdb' #3990

Open nreis9 opened 1 year ago

nreis9 commented 1 year ago
Screenshot 2023-03-07 at 5 06 52 PM

I am not sure where I can find the updated file.

nreis9 commented 1 year ago

I assumed the file changed to 'T4-lysozyme-L99A-p-xylene-implicit.pdb' but I got a couple of errors trying that pdb.

sef43 commented 1 year ago

This is similar to https://github.com/openmm/openmm/issues/3730

That file does not appear in the OpenMM code, looking at #3730 it comes from PDB file: https://www.rcsb.org/structure/4w52

peastman commented 1 year ago

That code is just showing how to parametrize something with GAFF. It's assumed that you have your own PDB file that you want to simulate.