Skip to content

Commit 06e186a

Browse files
authored
Update 02_molecular_setup.md
1 parent 508b926 commit 06e186a

1 file changed

Lines changed: 1 addition & 1 deletion

File tree

01_introduction/02_molecular_setup.md

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,7 @@ Unfortunately, many tools do a poor job in preparing PDB files, e.g. having quir
2222

2323
If pre-processing of the PDB file is required, then we recommend using one of the following third-party tools:
2424

25-
* [pdb4amber](https://github.com/Amber-MD/pdb4amber)
25+
* [pdb4amber](https://ambermd.org/tutorials/basic/tutorial9/index.php)
2626
* [PDBFixer](https://htmlpreview.github.io/?https://github.com/openmm/pdbfixer/blob/master/Manual.html)
2727

2828
When present, we do provide rudimentary support for `pdb4amber` via the `BioSimSpace.IO.reaadPDB` function, where passing the `pdb4amber=True` argument will pre-process the file with `pdb4amber` prior to creating a molecular system. However, we choose only to support the _default_ options, since many are experimental and have can have undesirable knock-on effects, e.g. using the `--add-missing-atoms` option strips all chain identifiers from the molecule.

0 commit comments

Comments
 (0)