Required Inputs Parameterization
Controlling Resource Consumption
Distributed Multipole Analysis and Electrostatic Single Point
Van der Waals Parameterization
Required Inputs Molecular Dynamics
Generic Molecular Dynamics Inputs
Available Integrators Barostats and Thermostats
- All booleans can switch their truth value, i.e., addhydrogens=True or addhydrogens=False
- For very large molecules initial opt, DMA and ESP may require large amounts of memory if quantum job consistently crashes
- Defaults are chosen specifically for maximizing accuracy and efficiency (without sacrificing accuracy)
- Be careful when changing optimization methods and coordinates without deleting previous XYZ files, DMA and ESP, fchk, cube files, this can cause eletrostaic fitting errors where your grid does not correspond to the potential file from the new coordaintes.
structure specifies input structure for poltype as an SDF file. Must include bond orders consistent with desired total charge. Default is None.
numproc specifies the number of processors allowed. Default will be 80% of total available on node.
maxmem specifies the maximum amount of RAM allowed. Default will be 80% of total available on node.
maxdisk specifies maximum scratch space allowed. Default will be 80% of total available on node.
consumptionratio specfies ratio of resources to use on node if not specified by user. Default is .8.
coresperjob specifies number of cores per job for jobs in parralel. Default is 2.
jobsatsametime specifies how many fragment jobs are allowed to run in parralel on node. Default is int(numproc/coresperjob) for input poltype job but 1 for fragment job.
coresperjob specifies number of cores per job for jobs in parralel. Default is 2.
parentjobsatsametime specifies number of input poltype jobs running on same host, rhis informs poltype how much resources to divide from available on the host. Default is 1.
addhydrogens specifies to adds hydrogens to unprotonated atoms. Default is False.
addhydrogentocharged specifies to add hydrogens to carbon with valence less than 4 and nitrogen with valence 2. Default is True.
genprotstatesonly specifies to output protonation states (at pH=7) in mol files(ProtonationState_0.mol, ...) and then exit. Default is False.
use_gaus specifies to use Gaussian for all QM calculations. Default is False.
atmidx specifies which number to start poltype type numbers from. Default is 401.
usesymtypes specifies to use symmetry typing to reduce and average atom types. Default is True.
indextotypefile specfies to use a file that will read in custom atom index to type number map. Default is None. Example indextotypefile=indextotypefile.txt. For each line in the file, the first item is atom index (starting from 1) and second item is the desired type number.
optbasisset specifies basis set for geometry optimization. Default is 6-31G*.
optmethod specifies quantum method for geometry optimziation. Default is MP2.
optpcm specifies to use PCM for geometry optimization. [True|False|auto] If set to auto, PCM will be used for zwitterion. Default is auto.
pcm_auto specifies to automatically activate PCM for zwitterions. If False, PCM will not be automatically activated. Default is True.
dontusepcm equivalent to pcm_auto=False.
use_gausoptonly specifies to only use gaussian for initial geometry optimization and Psi4 for all other QM steps. Default is False.
generateextendedconf specifies to use extended conformation for geometry optimization with torsions restrained. Default is True.
userconformation specifies to use the user input conformation for geometry optimization with torsions restrained. Default is False.
optloose specifies to use GAU_LOOSE optimization convergence criteria for psi4 optimization (both first geometry optimzation and for torsion geometry optimization)
optconvergence specifies optimization convergence. LOOSE, GAU_LOOSE criteria (identical to the keyword optloose); VERYLOOSE, only using gradient thresholds from GAU_LOOSE criteria. Default is LOOSE.
new_gdma specifies to use the new grid-based DMA algorithm. Default is False.
gdmacommand_* add/modify GDMA commands. For example, gdmacommand_Radius_S=0.80 will add the command Radius S 0.80 to GDMA input file.
usepoleditframes specifies to use POLEDIT frames rather than poltype frame detection. Default is True.
dmamethod specifies which quantum method to use for distributed multipole analysis (DMA). Default is MP2.
dmabasisset specifies basis set to use for quantum that generates initial multipoles. Default is 6-311G**.
espmethod specifies which quantum method to use for electrostatic fitting. Default is MP2.
espbasisset specifies basis set to use for electrostatic fitting. Default is aug-cc-pvtz.
numespconfs specifies number of conformations to be used for ESP potential fitting. Rdkit conformors are evaluated via MMFF94 energies and numespconfs-1 most favorable conformations are picked to add to fitting (with first being most extended conformation). Default is 1.
espextraconflist specifies list of conformors to add to extended conformation for ESP fitting. Default is to just use extended conformation for ESP fitting. Files can be SDF or any format as long as atom order is same as input molecule atom order.
indextompoleframefile specifies file of multipole frame definitions for each line (exactly how frames are defined in first key file). This will be used instead of poltype frame detection if specified.
writeoutmultipole specifies to write out multipole terms in pre-fit vdw key (from database matches). Default is True.
writeoutbond specifies to write out bond terms in pre-fit vdw key (from database matches). Default is True.
writeoutangle specifies to write out angle terms in pre-fit vdw key (from database matches). Default is True.
writeoutstrbnd specifies to write out strbnd terms in pre-fit vdw key (from database matches). Default is True.
writeoutopbend specifies to write out opbend terms in pre-fit vdw key (from database matches). Default is True.
writeoutvdw specifies to write out vdw terms in pre-fit vdw key (from database matches). Default is True.
writeoutpolarize specifies to write out polarize terms in pre-fit vdw key (from database matches). Default is True.
writeouttorsion specifies to write out torsion terms in pre-fit vdw key (from database matches). Default is True.
inputkeyfile specifies a keyfile to append parameters to pre-fit vdw key (from database matches). Default is None.
prmmodfile specifies (comma-separated list of) parameter modification patch file(s). See ParameterFiles/dma4_hfe2023.mod for example.
xtbtorresconstant specifies torsion restraint force constant for restraining dihedrals in xtb. Default is 5 kcal/mol/deg^2.
rotalltors specifies poltype to spin all rotatable bonds instead of transferring torsion parameters if found in database. Default is False.
torsppcm specifies poltype to use PCM for torsion SP. [True|False|auto] If set to auto, PCM will be used for zwitterion. Default is auto.
toroptpcm specifies poltype to use PCM for torsion optimization. [True|False|auto] If set to auto, PCM will be used for zwitterion. Default is auto.
dontdotor specifies poltype to skip torsion parameterization. Default is False.
torsionrestraint specifies how many kcals/mol/rad^2 to restrain other torsions around rotatable bond to be at current dihedral angle. Default is 1641.4 (.5 kcal/mol/deg^2).
foldnum specifies the number of fourier terms used in torsion fitting. Default is 6.
tordatapointsnum specifies the number of quantum jobs to sample along the dihedral angle for all torsions. Default is 12 if number of torsion parameters to fit is less than 12, else automatically adds more points.
toroptmethod specifies the opt method used for torsion parameterization. Default is xtb. toroptmethod=xtb will use semi empirical qm methods (not psi4 or gaussian). toroptmethod=ANI will use ANI for structure optimization. If toroptmethod=AMOEBA then AMOEBA minimized structure will be used instead of QM opt structure.
toroptmethodlist specifies a list of opt methods to use and can compare QM energy torsion profiles. By default toroptmethodlist only has toroptmethod as just one item in list.
torspmethodlist specifies a list of opt methods to use and can compare QM energy torsion profiles. By default torspmethodlist only has torspmethod as just one item in list.
xtbmethod specifies which xtb semi-empirical method to use, must have xtb turned on for either toroptmethod or torspmethod. Default is 2 (this corresponds to GFN2-xTB).
toroptbasisset specifies which basis set to use for geometry optimization during torsion parameterization. Default is 6-31G*.
torspmethod specifies the SP method for torsion parameterization. Default is wB97XD.torspmethod=xtb will use semi empirical qm methods (not psi4 or gaussian). torspmethod=ANI will use ANI for SP energies.
torspbasisset specifies which basis set to use for SP during torsion parameterization. Default is 6-311+G*.
onlyrotbndslist specifies to only rotate bonds in the list, onlyrotbndlist=1 2, 3 4, 5 6 . Default has no value.
dontrotbndslist specifies to not rotate bonds in the list, onlyrotbndlist=1 2, 3 4, 5 6 . Useful for modified AA lib, to tell poltype not to rotate backbone dihedrals. Default has no value.
tortor specifies to sample the torsion-torsion potential energy surface for two adjecent and rotatable dihedrals. Default is False.
onlyrottortorlist specifies list of tortors to rotate. "onlyrottortorlist=b1 c1 d1 , b2 c2 d2" where b1,c1,d1 belong tor tortor a1,b1,c1,d1,e1. Default has no value.
refinenonaroringtors specifies to pucker and refine torsion parameters on non-aromatic rings. Default is False.
nonaroringtor1Dscan specifies to cut a non-aromatic ring and spin the torsion for a 1D scan. Default behaviour is to transfer alkane torsion parameters.
fitfirsttorsionfoldphase specifies to add a phase fitting parameter to the first cosine term in the torsion fitting function. Default is False.
maxtorresnitrogen specifies number of dihedral restraints per rotatable bond for rotatable bonds that contain nitrogen dihedrals with hydrogens. Default is 1. For comparing different optimizers that may shift heavy atoms differently can set higher.
maxgrowthcycles specifies the maximum number of growth cycles before stopping fragmenter progtocol. Default is 4.
dontfrag specifies to not fragment input molecule. Default is False.
WBOtol specifies the tolerance for relative differences in Wiberg bond order between parent and fragment. Default is .05.
dovdwscan specifies to not refine initial guess vdw parameters from database assignment with ab initio dimer data. Default is False.
onlyvdwatomindex specifies to probe one vdw atom index on molecule. Default has no value.
accuratevdwsp specifies to use CBS extraction on MP2 with counterpoise on basis sets aug-cc-pV[TQ]Z. Default is False.
onlyvdwatomlist specifies list of Van der Waals atom indices to use in VdW refinement. Default has no value.
fixvdwtyperadii specifies list of vdwtypes to fix radius in fitting (can let other vdw parameters fit). Default has no value.
pdbcode specifies to take PDB code, downloads the crystal from RCSB and used Modeller to find missing residues and model them. Fast optimizaiton options are used by default. Missing residue information is found in REMARKS section of PDB which poltype reads. Default pdbcode is None.
usepdb2pqr specifies to use PDB2PQR program to compute pKa values for titratable residues via propka then will protonate the PDB for you and quit program. Default is False.
dockgridcenter specifies center in protein pocket to place ligand for docking. Default will use center of ligand.
dockgridsize specifies how far grid extends for docking. Default is dockgridsize=20,20,20 .
vinaexhaustiveness specifies how exaustive to search on grid for AutoDock Vina and vinardo. Default is 32.
nposes specifies number of poses for docking. Default is 10.
usevina specifies to use AutoDock Vina. Default is False.
usead4 specifies to use AutoDock 4. Default is False.
usevinardo specifies to use Vinardo scoring function. Default is False.
usegold specifies to use GOLD. Default is False.
gridspacing specifies grid density for AutoDock 4. Default is .4 angstroms.
ecrexpect specifies expected value of exponential distribution for exponential conensus ranking. This roughly controls how many molecules will be taken into consideration for consensus. Default is 10.
ligandxyzfilenamelist specifies the list of input tinker XYZ filename for the ligands. Default has no value.
keyfilenamelist specifies the list of input tinker key file for the ligand parameters. Default is None.
binding specifies to compute solvation and complexation free energies and combine for binding free energy. Default is False.
complexedproteinpdbname specifies complexed protein PDB file, needed for extracting the ligand and converting to tinker XYZ file. Make sure no atoms are missing!!. The atom order between ligand in this file and ligandxyzfile (tinker XYZ) needs to be same. Default has no value.
receptorligandxyzfilename specifies tinker XYZ file contains ligand and protein. This is automatically generated when the above complexedproteinpdbname is given. Default has no value.
solvation specifies to do solvation simulations. Default is False.
salthfe specifies whether to compute salt hydration free energy. Default is False.
neatliquidsim specifies to do neat liquid simualtion. Default is False.
annihilateligandxyzfilenamelist specifies the list of input tinker XYZ filename for the ligands that will be disappeared. Default is same as ligandxyzfilenamelist.
integrator specifies the MD integrator method. Default is RESPA.
thermostat specifies the thermostat method during NVT MD. Default is BUSSI.
barostatmethod specifies the barostat method used during NPT. Default is montecarlo.
vdwcutoff specifies the cutoff radius for van der Waals interactions. Units in angstroms. Default is 12.
ewaldcutoff specifies the cutoff radius for electrostatic interactions. Units in angstroms. Default is 7.
polareps specifies the Grid spacing for electrostatic potential surface. Default is .00001.
templateligandxyzfilename specifies input template tinker XYZ filename for aligning ligandxyzfilenamelist (first item in list) to templateligandxyzfilename. Program will quit after alignment. Default has no value.
externalapi specifies external script path for submitting MD jobs. Used with submitjobs.py. If user creates their own submission script, must edit submitjobs.py to work with it. Default is to submit jobs on local node. The submission script needs to be able to handle
correct assignment of tinker envioronments on whichever CPU/GPU cluster it operates on. If using RenLabCluster please read the file on https://github.com/bdw2292/RenLabCluster. Default has no value.
numproc specifies the number of threads to use for CPU dynamics. Default is 1.
prmfilepath specifies the path to parameters. Default is amoebabio18.prm.
simulationstostopfolderpath specifies a directory containing subdirectories of input jobs, recursive search will and *.end files to each folder with an *.arc file to stop simulations. Upon restarting program all *.end files that are in folders are automatically removed. Default has no value.
generatepdbtrajs specifies to convert ARC to PDB trajectory for equilibriated ARC and production dynamics ARC with full electrostatics and vdW. Default is True. Needs to be used with complexedproteinpdbname.
removesolventpdbtraj specifies to remove solvent (water/ions) from PDB trajectory. Used with generatepdbtrajs. Default is True.
useuniquefilenames specifies to use uniquefilenames for simulation files. Default is False, to make copying files between different folders easier.
heavyhyd specifies to use heavy-hydrogen tinker command
estimatedynamictimeonly specifies to quit program after estimating time to run simulations on current GPU. Default is False.
numbergpus specifies number of identical GPU's to use for estimating dynamic time. Default is 1.
- Verlet
integrator=verlet - Beeman
integrator=beeman - RESPA
integrator=respa - Stochastic
integrator=stochastic - Nose-Hoover NPT
integrator=nose-hoover
- Berendsen
barostat=berendsen - Monte-Carlo
barostat=montecarlo - Lagevin
barostat=Langevin
- Bussi-Parrinello
thermostat=bussi - Berendsen
thermostat=berendsen - Andersen Stochastic
thermostat=andersen - Nose-Hoover
thermostat=nose-hoover
makexyzonly specifies to only generate tinker XYZ from complexedproteinpdbname, ligandxyzfilenamelist and keyfilenamelist then the program will exit.
density specifies the density of neat liquid box in kg/m^3. Default has no value.
aaxis specifies the fixed box size for aaxis of PBC box. If not used, will be determined automatically. Default has no value.
baxis specifies the fixed box size for baxis of PBC box. If not used, will be determined automatically. Default has no value.
caxis specifies the fixed box size for caxis of PBC box. If not used, will be determined automatically. Default has no value.
listofsaltcons specifies the salt concentration for physiological systems. Units in mM. Default is [KCl]=100.
usepreequilibriatedbox specifies to use preequilibriated box and then cut default equilibriation time in half. Default is False.
boxonly specifies to stop program after making box. Default is False.
addphysioions specifies to add physiological ions to box system to mimic envioronment inside cell. Default is KCl at 100mM concentration.
restrainpositionconstant specifies the restraint position force constant during minimization for freezing the ligand and protein. Units in kcal/mol/Ang^2.
loosemincriteria specifies the convergence criteria for minimization, loose criteria. Units kcal/mol. Default is 10.
minonly specifies to quit after minimization is complete. Default is False.
minfinished specifies to skip minimization (for debugging). Default is False.
restrainatomgroup1 specifies the group of atoms (protein or ligand) used for tinker group restraints. If not specified, will be automatically determine (for group restraints during equilbriation). Default has no value.
restrainatomgroup2 specifies the group of atoms (protein or ligand) used for tinker group restraints. If not specified, will be automatically determine (for group restraints during equilbriation). Default has no value.
flatbotrest specifies whether to use flatbottom potential with group restraints. Default is True.
distancerestraintconstant specifies the restraint constant for restrain-distance keyword during production dynamics. Units in kcal/mol/Ang^2. Default is 10.
equilrestrainsphereradius specifies the sphere radius for protein atoms to restrain position during equilibriation. Units angstroms. Default is 2.
equiltimeNVT specifies the total time in NVT ensemble during equilbriation (for all temperatures combined except last temperature which is repeated by default). Units in ns. Default is 4.
equilrestlambdascheme specifies the group restraint force constants used during equilibriation (NVT). Default is 5,2,1,.5,.1,0.
equilibriatescheme specifies the temperature used for each NVT step during equilibriation. Units in K. Default is 50,100,150,200,300,300
equilwritefreq specifies how often to write out new frame during equilbriation MD. Units in ps. Default is 100.
equiltimestep specifies the MD time step during equilbriation. Units in fs. Default is 2.
equiltimeNPT specifies the total time in NPT ensemble (will determine average box length if using NVT production dynamics). Units in ns. Default is 1.
equiltimeionNPT specifies the total time in NPT ensemble for ion box when computing salt hydration free energy. Units in ns. Default is 1.
lastNVTequiltime specifies the last NVT equilibriation time longer than the previous ones. The previous ones are computed as equiltimeNVT/number_temperatures. Default is .5.
equilonly specifies to stop program after equilibriation and setup for production dynamics. Default is False.
equilfinished specifies to skip equilibration (for debugging). Default is False.
complexationonly specifies to only do equilibriation dynamics for complexation of host and guest (no solvation of ligand). Default is False.
productiondynamicsNVT specifies whether or not to use NVT ensemble during production dynamics. If on then will use NPT after equilbriating to determine average box size. Default is False.
restlambdascheme specifies the restraint lambda scheme during production dynamics. Default is 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.
vdwlambdascheme specifeis the Van der Waals lambda scheme during production dynamics. Default is 0,.45,.52,.56,.58,.6,.62,.64,.67,.7,.75,.8,.85,.9,.95,1,1,1,1,1,1,1,1,1,1,1,1.
estatlambdascheme specifies the electrostatics lambda scheme during production dynamics. Default is 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,.1,.2,.3,.4,.5,.6,.7,.8,.9,1,1.
proddynwritefreq specifies how often to write out new frame during production dynamics MD. Units in ps. Default is 2.
compproddyntime specifies the total time to run production dynamics (in NPT by default) for each lambda. Units in ns. Default is 10.
solvproddyntime specifies the total time to run production dynamics (in NPT by default) for each lambda. Units in ns. Default is 5.
proddyntime specifies the total time to run production dynamics (in NPT by default) for each lambda. Units in ns. Default is 5 for solvation and 10 ns for binding computations.
proddyntimestep specifies the MD time step during production dynamics. Units in fs. Default is 2.
checktraj specifies to check each trajectory for any corruption and delete if found. Default is False (slow to read each arc file).
prodmdfinished specifies to skip production dynamics (for debugging). Default is False.
alchemical specifies to do alchemical perturbation. Can turn this off if only want production dynamics will full electrostatics and vdw interactions turned on. Default is True.
complexationonly specifies to only do production dynamics for complexation of host and guest (no solvation of ligand). Default is False.
barinterval specifies how many times to recompute BAR over length of full production trajectory with evenly spaced chunks over the trajectory. Default is 5.
perturbkeyfilelist specifies a comma seperated list of keyfiles to add to end state and perturb with BAR. Right most item in the list is the end state. By default, arc file from nearestneighboring trajectory is used if fep is turned on, otherwise running MD for new state is default. Default has no value.
numinterpolsforperturbkeyfiles specifies a comma seperated list of number of interpolations per key file in perturbkeyfilelist (they should be same length). Use 1 for keyfiles that need only one interpolation (just between neighboring states), otherwise parameters will be interpolated via step=(b-a)/n where n is number of interpolations for that keyfile. Default is 1 for all keys in perturbkeyfilelist.
expfreeenergy specifies the experimental free energy for comparison in output tables. Default has no value.
fep specifies to copy nearest MD trajectory instead of running MD for each new keyfile to be perturbed. Used with perturbkeyfilelist keyword. Default is False.
pathtosims specifies path to folder containing subfolders of simulations for combining simulation data into one spreadsheet. Will exit program after combining data. Default has no value.
extractinterforbinding specifies to extract intermoleculer contribution to free energy for each BAR step. By default, annihilation is used which causes inter and intra molecular components to be mixed for binding free energy (gas phase is not computed since it would cancel in thermodynamic cycle). This keyword will extract the ligand dynamics and generate an ARC file for the ligand, run BAR and compute the exact intermolecular component to the free energy and add to spreadsheet.
barfilesfinished specifies to skip BAR (for debugging). Default is False.
redobar specifies to delete .bar files and redo BAR!