Tools comparison: ms_top2pdbs vs get_aver_pqr

[CatChenal]

Comparison between ms_top2pdbs and get_aver_pqr

Commonality: Both tools output pqr files

Tool:	ms_top2pdbs	get_aver_pqr
Purpose	Mostly used for H-bond analysis where a large number of microstates pdbs are needed (and the pqr files are just extra output)	Used to obtain a pqr file, which can either have the Boltzmann-averaged charges or those of the most-occupied conformers, which can be used for comparing with a cryo-EM map
Output	User-defined N pdb and pqr files (default N: 5)	One pqr file, which can be that of the Boltzmann average (default) or that of the most occupied conformers
Data Source	Microstates (hence the 'ms' prefix) in the msout file for a given pH/Eh point, and step2_out.pdb data	The occupancy table (fort.38) at a given pH/Eh point and ste2_out.pdb data
Implications	Requires that the ms_out folder is preserved in Step 4.	No ms_out requirement
Speed	Slowish due to the overhead of processing all microstates	Fast