Hello,
i am new to OpenMM, so if the fix is obvious please don't go too hard on me.
I created a PDB file with Avogadro, which works perfectly fine in VMD or PyMOL, but when i try to open it with app.PDBFile(), it somehow only loads two of the 33 Atoms??
I attached a screenshot of the python code which shows the problem, and also the PDB File i am talking about (only not saved as .pdb, since you cant upload that here)
Thank you very much, and best regards,
Dominik
PDB File doesnt properly turn into topology with app.PDBFile
- Dominik St. Pierre
- Posts: 2
- Joined: Thu Apr 18, 2024 7:28 am
PDB File doesnt properly turn into topology with app.PDBFile
- Attachments
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- 1E4Mcyclohexane.pdb.txt
- (5.03 KiB) Downloaded 145 times
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- See topology and positions output at the very bottom
- Bildschirmfoto vom 2024-04-18 16-31-00.png (405.33 KiB) Viewed 1734 times
- Peter Eastman
- Posts: 2562
- Joined: Thu Aug 09, 2007 1:25 pm
Re: PDB File doesnt properly turn into topology with app.PDBFile
Every atom in a residue is required to have a unique name. Because your atoms are all named either "H" or "C", it assumes they are alternate locations for the same two atoms rather than different atoms.
- Dominik St. Pierre
- Posts: 2
- Joined: Thu Apr 18, 2024 7:28 am
Re: PDB File doesnt properly turn into topology with app.PDBFile
Thank you so much!!!