FlexAID

Compile FlexAID using CMake:

git clone --branch flexaid-cpp https://github.com/NRGlab/FlexAID
cd FlexAID
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=Release
cmake --build . --target FlexAID -j 4

FlexAID requires a config and ga file to run. These can be generated using ProcessLigand (installed with pypi: pip install processligand-py). When using ProcessLigand make sure atom_index=90000 on the ligand.

Required Config file codes

Code	Description	Value
INPLIG	Ligand input file	Absolute path to ligand .inp file
METOPT	Optimization method	GA
OPTIMZ	Ligand Flexible residues	One line for each flexible bond in the ligand
PDBNAM	Target input file	Absolute path to target .inp.pdb file
RNGOPT	Binding site file	GLOBAL or LOCCLF + Absolute path to binding site _sph_ file

More details for OPTMIZ:

This line appears at least once for the rigid docking search. Each line contains the ID of the residue to be optimized (AAA – NNNN), followed by an integer number. This number is the number of the rotatable bond to be optimized or a zero for the ligand to be docked. For example, OPTIMZ 132 – 0 defines that residue 132 chain “ “ is the ligand to be docked.

Adding the following lines, you would be setting flexible the first rotatable bond of the ligand and the second flexible bond of the residue whose number is 76, chain A:

OPTIMZ 132 – 1

OPTIMZ 76 A 2

When using ProcessLigand the residue number is typically 9999 and at least 2 lines of OPTIMZ are required:

OPTIMZ 9999 – -1

OPTIMZ 9999 – 0

Additionally, one line is required for each line with FLEDIH in the ProcessLigand output.

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Optional Config file codes

Code	Description	Value
ACSWEI
BPKENM
CLRMSD
CLUSTA		FO or DP or CF (Typically not set)
COMPLF	Complementarity function to use	SPH or VCT
CONSTR
DEECLA
DEEFLX
DEFTYP
DEPSPA
EXCHET
FLEXSC	Target flexibility	One line per flexible residue (Residue number, chain, Residue name). Example: 196 A HIS
HTPMOD	Makes printing and file writing minimal for use in a high throughput way	N/A
IMATRX	Matrix file to be loaded	Absolute path to matrix file
INCHOH
INTRAF
MAXRES	Maximum number of results to output	10
NMAAMP
NMAEIG
NMAMOD
NOINTR
NORMAR
NRGOUT	Time FlexAID waits before aborting when NRGSUI option is specified	60 (seconds)
NRGSUI	Writes a .update file and waits for it to be deleted before continuing	N/A
OMITBU
OUTRNG
PERMEA	Permeability	0.9
RMSDST	Reference for calculating RMSD	Absolute path to ligand _ref.pdb file
ROTOBS
ROTOUT
ROTPER
SCOLIG
SCOOUT
SLVTYP	User specified atom type for solvent	40
SLVPEN
SPACER	Spacer length	0.375
STATEP	Path to folder where Pause and Abort files can be written.	Absolute path
TEMPER
TEMPOP	Temp folder path	Absolute path to temp folder (typically inside the STATEP folder)
USEACS
USEDEE
VARANG	Delta angle	5.0
VARDIS
VARDIH	Delta dihedral	5.0
VARFLX	Delta flexibility	10.0
VCTPLA
VCTSCO
VINDEX

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GA Codes

Code	Description	Value
NUMCHROM	Number of chromosomes	(int)
NUMGENER	Number of generations	(int)
ADAPTVGA
ADAPTKCO		(list) with 4 floats
CROSRATE
MUTARATE	Mutation rate
POPINIMT	Population initialization method	RANDOM or IPFILE
FITMODEL	Fitness model	PSHARE or LINEAR
SHAREALF	Sharing Parameter α
SHAREPEK	Sharing parameter peaks
SHARESCL	Sharing scaling
STRTSEED	Set a custom starting seed	(int)
REPMODEL	Reproduction technique code	STEADY, BOOM
BOOMFRAC	Population boom size (fraction of the number of chromosomes)	0 to 1 (float)
PRINTCHR	Number of best chromosome to print each generation	(int)
PRINTINT	Print generation progress as well as current best cf	0 or 1
OUTGENER