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	-1 Invalid URL	127.0.0.1 Status	Custom Parallel Analysis	http://127.0.0.1:8787/status
4	404 Not Found	align_structure	Examples - README	https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb
5	404 Not Found	align_trajectory_first	Examples - README	https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/aligning_trajectory_to_first_frame.ipynb
6	404 Not Found	align_trajectory	Examples - README	https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/aligning_trajectory.ipynb
7	404 Not Found	rmsf	Examples - README	https://userguide.mdanalysis.org/examples/analysis/alignment_and_rms/rmsf.ipynb
8	-1 Invalid URL	Localhost 8000	Contributing Docs	http://localhost:8000/
9	404 Not Found	Pydagogue	Contributing	https://matthew-brett.github.com/pydagogue/
10	403 Forbidden	AKMA Documentation	DCD Lammps	https://academiccharmm.org/
11	SSL Certificate	Jmol	Selection Exporters	https://wiki.jmol.org/index.php/Main_Page
12	404 Not Found	Image Src	Constructing Universe	https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true
13	404 Not Found	Software Carpentry Test	Testing	https://software-carpentry.org/4_0/test
14	404 Not Found	DataFrame	RMSD Analysis	https://pandas.pydata.org/pandas-docs/stable/getting_started/dsintro.html
15	403 Forbidden	TandF Reference	References	https://www.tandfonline.com/doi/abs/10.1080/07391102.2000.10506570
16	403 Forbidden	TandF Reference	References	https://www.tandfonline.com/doi/abs/10.1080/00401706.1962.10490022
17	-1 Not Found	MMTF	MMTF Format	https://mmtf.rcsb.org/
18	-1 Not Found	HOOMD-blue	GSD Format	http://codeblue.umich.edu/hoomd-blue/index.html
19	Too Many Redirections	Springer Book	References	https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Fbook%2F10.1007%2Fb98835
20	-1 Not Found	XML	XML Format	http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html
21	-1 Not Found	GAMESS-UK	GMS Format	http://www.cfs.dl.ac.uk/
22	404 Not Found	MOL2	MOL2 Format	http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
23	-1 Not Found	FHI-aims	IN Format	https://aimsclub.fhi-berlin.mpg.de/
24	404 Not Found	PQR	PQR Format	https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html
25	404 Not Found	PDB2PQR	PQR Format	https://apbs-pdb2pqr.readthedocs.io/en/latest/pdb2pqr/index.html
26	404 Not Found	APBS	PQR Format	https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/index.html
27	-1 Not Found	CRD	CRD Format	https://www.charmmtutorial.org/index.php/CHARMM:The_Basics
28	404 Not Found	PARM	TOP Format	https://ambermd.org/formats.html
29	-1 Not Found	IBIsCO	TRZ Format	http://www.theo.chemie.tu-darmstadt.de/ibisco/IBISCO.html
30	-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).