Tool Set Documentation

CHARMM Parameters

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bomlevundefset bomb level
prnlevundefset print level
ioformatundefset ioformat: 'exte' or 'noex'
param36parameter set: 19 (CHARMM19), 22 (CHARMM22), opls, a94 (amber 94), eef1, mmff, eef1.1
xtopundefextra topology files
xparundefextra parameter files
pstreamundefextra topology/parameter files to be streamed
parflexundefadd 'flex' when reading parameters/topologies
blockedundefblocked termini
nterundefN-terminus, requires blocked
cterundefC-terminus, requires blocked
nuc3terundefnucleic acid 3" terminus
nuc5terundefnucleic acid 5" terminus
deoxy1deoxy patch for nucleic acids
terlistundefexplicit list of termini, format: SEG:FIRST:LAST[=...]
fixcoo1fix COO if necessary
hsd""list of HSD residues
hse""list of HSE residues
hsp""list of HSP residues
resmod""list of residue name modifications
patch""list of patches
autogen1auto generate angles/dihedrals after patches
buildall1rebuild all missing atoms
faster"on"fast energy routines (on|off)
dielec'CDIE'dielectric response CDIE (const.) or RDIE (distant dep.)
epsilon1.0dielectric constant for non-bonded interactions
cutnbundefcutoff for non-bonded list generation
cutoffundefcutoff for non-bonded interactions
cutonundefonset of switching function for non-bonded interaction
cutimundefcutoff for image atoms
cut1use cutoff
crystalcutundefcutoff for crystal
nbmode"atom"atom or group
vdwlrc0van der Waals long range correction
softvdw0soft van der Waals core
softemaxundefmaximum van der Waals energy
softmineundefminimum attractive energy
softmaxeundefmaximum electrostatic energy
user1USER energy term
cmap1CMAP energy term
echeck20.0energy tolerance check for dynamics
ace0ACE implicit solvation
aceieps1.0ACE internal dielectric
aceseps80.0ACE external dielectric
acealpha1.3ACE alpha
acesigmaundefACE sigma
acevscale1.0ACE volume scale
sasagamma0.00542gamma for SASA
sasadelta0.920delta for SASA
gbundefGeneralized Born implicit solvent: bgb, gbmf, gbmf2, gbmva, gbmvg
gbeps80.0epsilon in GB prefactor
gbcrad0.91BGB radius scaling of main chain carbon w/ param19
gbhrad0.8BGB radius scaling of hydrogen atoms w/ param22
gblambdaundefBGB lambda factor
gbmvadundefGBMVA shift
gbmvadeundefGBMVA eshift
gbmvasundefGBMVA slope
gbmval10.5GBMVA lambda 1
gbmvap10.45GBMVA P1
gbmvap21.25GBMVA P2
gbmvap30.65GBMVA P3 (old: 0.70)
gbmvap4undefGBMVA P4
gbmvap5undefGBMVA P5
gbmvap68.0GBMVA P6, Still's factor
gbmvap7undefGBMVA P7, VSA adjustment
gbmvaig32GBMVA integration grid size
gbmvafrqundefGBMVA alpha update frequency
gbmvdrfrqundefGBMVA surface integration point update frequency
gbmvaimpundefGBMVA impulse derivatives
gbmvaempundefGBMVA exponentially damped impulse
gbmvarithundefGBMVA arithmetic mean: alpha_ij = alpha_i+alpha_j
gbmvabuf0.2GBMVA buffer for dynamics
gbmvabeta-12GBMVA beta parameter (old: -20)
gbmvaonx1.9GBMVA OnX parameter
gbmvaoffx2.1GBMVA OffX parameter
gbmvacubicundefGBMVA cubic VSA
gbmvacorr1GBMVA r7 correction (1) or r5 correction (0)
gbmvaextraundefGBMVA extra commands
gbmvagcutundefGBMVA GCUT (1 or 2)
gbmvakappaundefGBMVA kappa
gbmvafastundefGBMVA FAST
gbmvasgbfrq4GBMVA SGBFRQ
gbmvasxd0.3GBMVA SGBFRQ delta
gbmva1undefGBMV A1 parameter
gbmva2undefGBMV A2 parameter
gbmva3undefGBMV A3 parameter
gbmva4undefGBMV A4 parameter
gbmva5undefGBMV A5 parameter
gbmvdfundefGBMV adjustment factor for shift
gbmvdoffundefGBMV epsilon offset for shift adjustment
gbmvmstlundefGBMV modified Still
gbmvms01.0GBMV MS0 parameter
gbmvms10.0GBMV MS1 parameter
gbmvms20.0GBMV MS2 parameter
gbmvms30.0GBMV MS3 parameter
gbmvdefmnp0turn on default membrane non-polar profile
gbmvzs0.5parameters for membrane non-polar profile
gbmvzm9.2parameters for membrane non-polar profile
gbmvzt25parameters for membrane non-polar profile
gbmvst0.32parameters for membrane non-polar profile
gbmvepsundefGBMV solvent dielectric
gbmvepsuundefGBMV solute ref dielectric
gbmvduundefGBMV adj. delta for solute dielectric
gbmvsa0.015GBMV hydrophobic SASA term factor
gbmvsb0.900GBMV hydrophobic SASA term offset
gbmvsagbundefGBMV hydrophobic SASA term on a selection basis
gbmvason1.2GBMV SASA internal parameter, old: 0.5
gbmvasoff1.5GBMV SASA internal parameter, old: 1.75
#gbmvexcl0GBMV selection
gbswsw0.3GBSW switching length
gbswrmax20.0GBSW maximum integration radius
gbswnang38GBSW number of angular integration points
gbswnrad0GBSW number of radial integration points
gbswsgamma0.00GBSW surface tension coefficient
gbswdgp1.5GBSW grid spacing for lookup table
gbswrbuffer0.0GBSW buffer region for lookup table
gbswtmemb0.0GBSW thickness of membrane
gbswmsw0.3GBSW membrane switching length
gbswms0GBSW molecular surface approx.
hdgbprofileundefepsilon profile for HDGB
hdgbnpprofileundefnon-polar profile for HDGB
hdgbdensh2oprofileundefdensity profile for water (HDGB van der Waals)
hdgbdensoprofileundefdensity profile for O (HDGB van der Waals)
hdgbdenscprofileundefdensity profile for C (HDGB van der Waals)
hdgbdensccprofileundefdensity profile for CC (HDGB van der Waals)
hdgbdenshprofileundefdensity profile for H (HDGB van der Waals)
hdgbvdw0turn on HDGB van der Waals term
hdgbvdwact30.25HDGB van der Waals a for CT3
hdgbvdwacy0.2HDGB van der Waals a for CY
hdgbvdwacph0.4HDGB van der Waals a for CPH
hdgbvdwacc0.4HDGB van der Waals a for CC
hdgbvdwaca0.2HDGB van der Waals a for CA
hdgbvdwact10.55HDGB van der Waals a for CT1
hdgbvdwact20.45HDGB van der Waals a for CT2
hdgbvdwacm0.7HDGB van der Waals a for CM
hdgbvdwahs0.5HDGB van der Waals a for HS
hdgbvdwaho0.75HDGB van der Waals a for HO
hdgbvdwahy0.2HDGB van der Waals a for HY
hdgbvdwahm0.675HDGB van der Waals a for HM
hdgbvdwahp0.15HDGB van der Waals a for HP
hdgbvdwahr0.475HDGB van der Waals a for HR
hdgbvdwanh0.225HDGB van der Waals a for NH
hdgbvdwany0.15HDGB van der Waals a for NY
hdgbvdwaoh0.75HDGB van der Waals a for OH
hdgbvdwaoy0.725HDGB van der Waals a for OY
hdgbvdwaor0.425HDGB van der Waals a for OR
hdgbvdwasm0.175HDGB van der Waals a for SM
hdgbvdwasc0.425HDGB van der Waals a for SC
hdgbvdwas0.225HDGB van der Waals a for S
hdgbvdwap0.375HDGB van der Waals a for P
scalerad0scaled radii for GB/PB
dcel0.5PB grid spacing
epsw80.0epsilon for solvent
epsp1.0epsilon for solute
epsprundefepsilon for solute reference if set
epsr1.0epsilon for reference environment
smooth0smooth boundary
pbdelta8.0distance to boundary
proberad1.4water probe radius
pbionr2.0ion exclusion radius
pbionconc0.0ion concentration
pbextra""extra parameters for PBEQ
pbepsfileundefexternal file for dielectric grid (first type)
pbepsgridundefexternal file for dielectric grid (second type)
chargefileundefload charges from external file
volumespace200000space for volume calculation
rdfrmaxundefmaximum radius for RDF analysis
rdfbins100number of bins for RDF analysis
rdfspfac10space allocation for RDF analysis
rdfvolumeundefnormalization volume for RDF analysis
rdfexcludeundefbygr, byres, byseg to exclude self pairs
diffrangeundefdistance range for diffusion calculation
ncors20number of time steps for diffusion/correlation calculation
puckermode"AS"AS or CP pucker calculation
ptype"P1"P1 or P2 correlation
sradfac1.0overall scaling factor for GB/PB radii
sbackn1.00.90, # peptide backbone N scaling factor
sbacko1.00.94, # peptide backbone O scaling factor
sbackca1.0peptide backbone CA scaling factor
mfnhundefradius for H*
mfn3undefradius for ch3
mfn2undefradius for cb
mfnb10undefradius for backbone CA (GLY)
mfnb9undefradius for backbone CA
mfnb6undefradius for backbone C
mfnb7undefradius for backbone O
mfnb8undefradius for backbone N
mfn5undefradius for ch
mfn13undefradius for roh
mfn12undefradius for oh
mfn4undefradius for cet
mfn19undefradius for crh
mfn18undefradius for cpro
mfn7undefradius for ctrp
mfn16undefradius for ntrp
mfn8undefradius for css
mfn17undefradius for sulfur
mfn25undefradius for s2
mfn6undefradius for cam
mfn15undefradius for nam
mfn11undefradius for oam
mfn10undefradius for ocar
mfn9undefradius for cze
mfn14undefradius for nal
mfn21undefradius for nhis
nina9undefradius for ARG CZ
nina9lundefradius for LYS CE
nina10undefradius for GLU/ASP OE*/OD*
nina11undefradius for ASN/GLN OE*/OD*
nina14undefradius for ARG NH*/NE
nina14lundefradisu for LYS NZ
nina7undefradius for TRP CE*/CD*/CZ*/CH2
nina16undefradius for TRP NE1
nina12undefradius for OG*
nina3undefradius for CG*
ninahundefradius for H*
ninab1undefradius for backbone CAY/CAT
ninab2undefradius for backbone CY
ninab3undefradius for backbone OY
ninab4undefradius for backbone NT
ninab5undefradius for backbone OT*
ninab6undefradius for backbone C
ninab7undefradius for backbone O
ninab8undefradius for backbone N
ninab9undefradius for backbone CA
ninab10undefradius for backbone CA (GLY)
nina2undefradius for CB
nina4undefradius for GLU CG
nina5undefradius for CD*
nina6undefradius for GLN CD/ASN CG/GLU CD/ASP CG
nina18undefradius for PRO GB/CG/CD
nina19undefradius for TYR/PHE CE*/CD*/CZ
nina8undefradius for MET CE
nina20undefradius for HSD CE1/HSD CD2
nina13undefradius for TYR OH
nina21undefradius for HSD NE2/ND1
nina22undefradius for HSP NE2/ND1
nina15undefradius for GLN NE2/ASN ND2
nina17undefradius for S*
asp0flag to switch on ASP energy terms
aspfileundefexternal input file for ASP energy term
aspval5.42ASP solvation parameter
aspvalcundefASP solvation parameter for carbon atoms
aspvalnundefASP solvation parameter for nitrogen atoms
aspvaloundefASP solvation parameter for oxygen atoms
aspvalhundefASP solvation parameter for hydrogen atoms
aspvalsundefASP solvation parameter for sulphur atoms
aspradhundefASP hydrogen radius
aspref0.0ASP reference area
og0flag to switch on Olgun's energy score
eef10flag to switch on EEF1 energy terms
eef1file"solvpar.inp"EEF1 parameter file
imm10implicit membrane model based on EEF1, use eef1file for loading parameter file
imm1p360imm1 model with using CHARMM36 all-atom parameters
imm1file"solvpar.inp"IMM1 parameter file
imm1width26.0membrane width
imm1aemp0.85parameter a
sasa0flag to switch on SASA energy terms
sasaeps2.0SASA dielectric constant
sasasig1-0.060SASA sig 1 value
sasasig20.012SASA sig 2 value
sasasig30.00SASA sig 3 value
sdsteps50number of minimization steps for steepest descent min.
sdstepsz0.005initial step size for steepest descent min.
updnbsd-1update freq. for non-bonded list in steepest descent min.
minmode"abnr"minimization protocol
minsteps500number of minimization steps for min.
minstepsz0.005initial step size for min.
minetol1.0E-5energy tolerance for min.
minupdnb-1update freq. for non-bonded list in min.
minoutfrq10output freq. for minimization runs
shake0use shake
shaketol1.0E-8shake tolerance
shakemode'hyd''hyd'rogen or 'all' atoms are restrained
shakefast0use fast vector/parallel version of shake
periodicundefuse periodic boundaries
explicit1do not use implicit solvent for explicit solvent
solventundefresidue names of solvent molecules for PBC
imbysegundefresidue images by segment
imbyresundefresidue images by residue
imbysegx0.0center for images by segment
imbysegy0.0center for images by segment
imbysegz0.0center for images by segment
imbyresx0.0center for images by segment
imbyresy0.0center for images by segment
imbyresz0.0center for images by segment
ewald1use Ewald for explicit solvent
pmekappaundef0.32, # PME distribution width
pmekmax5.05.0, # PME K max
npmeundef64, # number of grid points for PME grid
npmexundefnumber of grid points in x direction
npmeyundefnumber of grid points in y direction
npmezundefnumber of grid points in z direction
boxshapeundefbox shape for periodic boundaries
boxsizeundefbox size
boxxundefbox x dimension
boxyundefbox y dimension
boxzundefbox z dimension
dynens'NVT'dynamics ensemble 'NVT', 'NPT', 'NPH', 'NVE'
dynber0use Berendsen thermostat
dynbertc5.0coupling constant for Berendsen
dynnoseundefuse Nose-Hoover thermostat
dynnoseq50.0Nose-Hoover qref
dynnosen5Nose-Hoover ncyc
dynintegundefovverride default integrator choices: leap, vver, vv2
dyntstep0.002dynamics time step in picoseconds
dynsteps100dynamics steps
dyntemp298dynamics temperature
dynitempundefinitial temperature for heating/equilibration
dynseedundefdynamics random seed
dyndeltat10.0temperature change during heating/cooling
dynhtfrq-1temperature change frequency
dyntrfrqundeftrans/rot removal frequency
dyneqfrq200equilibration frequency
dyntwin5.0temperature window during equilibrition
dynscaleundeftemperature scaling factor for restarts
dynoutfrqundeffrequency of energy/trajectory output
dynupdnb-1update of non-bonded list
dynupdimg-1update of images
dynpress1.00the pressure (in atm) for NPT simulations
dynpgamma25.0gamma value for NPT simulations
dynpmass400.0Langevin piston mass for NPT simulations
dynpext0Use external virial in NPT simulations
nblisttype"bycb"non-bonded list generation
dynconsundefKDYN dynamics
dynkmas0.1KDYN dynamics mass
dynkfkcundefKDYN FKC
dynkdkcundefKDYN DKC
phmdparundefPHMD parameter file
phmdph7.0simulation pH
phmdpri1000print output file every 1000 steps
phmdmass10.0mass for the titration and tautomer interconversion coordinates
phmdbarr2.5titration barrier
phmdbartau2.5tautomer interconversion barrier
phmdtemp298PHMD temperature
phmdout"final.lamb"output file of lambda values
phmdderiundefcompute derivatives
phmdthetaundeftheta value if phmdderi defined
phmdthetaxundefthetax value if phmdderi defined
phmdselundefselection of titrating residues
sgmd0self-guided MD
sgmddrag0.2SGMD drag force
sgmdavg1.0SGMD average?
sgmdvfb-1.0SGMD ?
sgmdfrq1SGMD update frequency
sgld0self-guided Langevin dynamics
sgbz0option for SGLDfp simulation (Boltzman Dist.)
sgldtsvg0.2local avg time
sgldtsvp10guiding effect avg time
sgldtpsg1.0giding temperature
sgldsgft0.0guiding factor
sgldsgmv0allow guiding force on center of mass
sgldistr1index of the first atom for guiding force application
sgldiend"natom"index of the last atom for guiding force application
noerestundeffile name with NOE restraint commands
xnoerestundefX-plor file name with NOE restraint commands
noerexp3exponent for distance averaging
noekmin1.0force constant for small distance harmonic potential
noekmax1.0force constant for large distance harmonic potential
noefmax9999.0maximum force
noescale1.0overall scaling factor
noemindist0use minimum distance for multiple atoms
nlambda10number of windows for PERT sampling
pequi1000number of equilibration steps
pprod4000number of production steps
ilambdaundefrun individual lambda step (0 .. nlambda)
#qfep0charging FEP
#qfepfix1fix segment
dynextraundefextra dynamics command
qcorundefEwald charge correction
whamtol0.001WHAM tolerance
whamsteps200WHAM iteration steps
whammaxtime1000000WHAM maximum time
whammaxwin200WHAM maximum number of windows
tamd0Turn on torsion-angle MD, also turns on Berendsen heat bath
tamdsetupundefTorsion-angle MD tree setup code, standard tree setup if not given
dyntpundefturn on TP control
dyntpcmda0TPControl dampening of center of mass motion
dyntptau0.05characteristic thermostat response time in ps
dyntppress1.0set reference pressure
dyntpbtau0.05characteristic barostat response time in ps
lang0flag for running Langevin dynamics
langrbuf0.0radius of Langevin inner buffer sphere
langfbeta5.0friction coefficient for Langevin dynamics
langselundefCHARMM atom selection to apply Langevin friction
langfileundeffile for setting friction coefficients
langupdundefupdate of Langevin region
mcprmc0turn on MC barostat
mctens0.0MC barostat reference surface tension
mcprzz1.0MC barostat pressure in atm at z dimension
mciprsf15.0MC barostat sampling frequency
openmm0turn on to use openMM