FESetup cannot find maximum commen substructure even when timeout is set to no time out

[ppxasjsm]

When trying to compute the morph between two ligands FESetup struggles to find the maximum common substructure and will therefore propose a buggy morph. The first image shows the two pdb files of the ligands to be morphed. The next shows the resulting morphed ligand: The identified MCS looks like this:

FESetup input looks like this:

FE_type = Sire
AFE.separate_vdw_elec = False
mcs.match_by = spatially-closest
mcs.timeout = 0

[globals]
forcefield = amber, ff14SB, tip3p
gaff = gaff2
logfile = CatS_30.log

[ligand]
basedir = poses
file.name = ligand.pdb
molecules = CatS_30, CatS_29

box.type = rectangular
box.length = 12.0
neutralize = yes

min.nsteps = 1000
min.restr_force = 10.0
min.restraint = notsolvent

md.heat.nsteps = 1000
md.heat.restr_force = 10.0
md.heat.restraint = notsolvent

md.constT.nsteps = 1000
md.constT.restr_force = 10.0
md.constT.restraint = notsolvent

md.press.T = 298.0
md.press.nsteps = 20000
md.press.p = 1.0

morph_pairs = CatS_29 > CatS_30

[protein]
basedir = protein
file.name = protein.pdb
molecules = cats

[complex]
pairs = cats : CatS_30

box.type = rectangular

The zip archive contains all relevant coordinate files.

FESetup.zip

[skfegan]

Thanks for the input files. I will have to track down the bug in the use of the match_by keyword.

[skfegan]

You might want to try match_by = shapealign instead of match_by = spatially-closest

[jaechanglim]

Is it solved? what is the default value of match_by?