Fix Dead Links in MDAnalysis User Guide Documentation

[mhmohona]

I checked MDAnalysis User Guide - Stable Index and found several links that are either broken, lead to 404 errors, or are inaccessible. Below is a table summarizing the problematic links, including the pages where they are found and the anchor text associated with them.

#	Error	Anchor Text	Linked From	Broken Link
1	404 Not Found	HOLE2 MDAKit	Releases	https://www.mdanalysis.org/hole2-mdakit/
2	404 Not Found	@g2707	Releases	https://github.com/g2707
3	404 Not Found	align_structure	Examples - README	https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb
4	404 Not Found	align_trajectory_first	Examples - README	https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/aligning_trajectory_to_first_frame.ipynb
5	404 Not Found	align_trajectory	Examples - README	https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/aligning_trajectory.ipynb
6	404 Not Found	rmsf	Examples - README	https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/rmsf.ipynb
7	404 Not Found	Pydagogue	Contributing	https://matthew-brett.github.com/pydagogue/
8	404 Not Found	DataFrame	RMSD Analysis	https://pandas.pydata.org/pandas-docs/stable/getting_started/dsintro.html
9	-1 Not Found	MMTF	MMTF Format	https://mmtf.rcsb.org/
10	-1 Not Found	HOOMD-blue	GSD Format	http://codeblue.umich.edu/hoomd-blue/index.html
11	-1 Not Found	XML	XML Format	http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html
12	-1 Not Found	GAMESS-UK	GMS Format	http://www.cfs.dl.ac.uk/
13	404 Not Found	MOL2	MOL2 Format	http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
14	-1 Not Found	FHI-aims	IN Format	https://aimsclub.fhi-berlin.mpg.de/
15	404 Not Found	PQR	PQR Format	https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html
16	404 Not Found	PDB2PQR	PQR Format	https://apbs-pdb2pqr.readthedocs.io/en/latest/pdb2pqr/index.html
17	404 Not Found	APBS	PQR Format	https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/index.html
18	-1 Not Found	CRD	CRD Format	https://www.charmmtutorial.org/index.php/CHARMM:The_Basics
19	404 Not Found	PARM	TOP Format	https://ambermd.org/formats.html
20	-1 Not Found	IBIsCO	TRZ Format	http://www.theo.chemie.tu-darmstadt.de/ibisco/IBISCO.html
21	-1 Not Found	YASP	TRZ Format	http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html

I am ready to start working on fixing these issues, but I would appreciate some feedback or suggestions before proceeding. Also, if there are preferred sources to replace outdated links, please provide them.

[RMeli]

@mhmohona that is fantastic investigative work, thank you for doing this. I think it would be great to fix the broken links for sure. Tracking down the new links with Google is probably the best course of action; the old link should give you already quite a bit of information.

For example, Googling

hole2-mdakit

the first hit is the GitHub repository of mdahole2, while the second hit is already the link we want: https://mdakits.mdanalysis.org/mdahole2.html (i.e. a link to the official MDAnalysis MDAKit repository for the hole2 MDAKit).

[mhmohona]

I wasn't able to fix the broken links in https://userguide.mdanalysis.org/stable/formats/format_reference.html because I couldn't find the correct links for row number 11 through 21.

[RMeli]

Hi @mhmohona, what have you tried in these cases? 11 through 21 seems to be linked to specific file formats of different software. Have you looked into the documentation of said software? The most likely cause of the link breakage is that the page about the file format has moved within the documentation of the software (or that the documentation of the software has moved all together).