| bomlev |
undef |
set bomb level |
| prnlev |
undef |
set print level |
| |
| param |
27 |
parameter set: 19 (CHARMM19), 22 (CHARMM22), opls, a94 (amber 94), eef1, mmff |
| |
| xtop |
undef |
extra topology files |
| xpar |
undef |
extra parameter files |
| |
| blocked |
undef |
blocked termini |
| nter |
undef |
N-terminus, requires blocked |
| |
| nuc3ter |
undef |
nucleic acid 3" terminus |
| nuc5ter |
undef |
nucleic acid 5" terminus |
| deoxy |
1 |
deoxy patch for nucleic acids |
| terlist |
undef |
explicit list of termini, format: SEG:FIRST:LAST[=...] |
| |
| 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 |
| autogen |
1 |
auto generate angles/dihedrals after patches |
| |
| buildall |
1 |
rebuild all missing atoms |
| |
| faster |
"on" |
fast energy routines (on|off) |
| |
| dielec |
'CDIE' |
dielectric response CDIE (const.) or RDIE (distant dep.) |
| epsilon |
1.0 |
dielectric constant for non-bonded interactions |
| cutnb |
undef |
cutoff for non-bonded list generation |
| cutoff |
undef |
cutoff for non-bonded interactions |
| cuton |
undef |
onset of switching function for non-bonded interaction |
| cut |
1 |
use cutoff |
| trunc |
undef |
shift/fshift/switch/fswitch |
| vtrunc |
undef |
vshift/vfshift/vswitch/vfswitch |
| nbmode |
"atom" |
atom or group |
| vdwlrc |
0 |
van der Waals long range correction |
| |
| user |
1 |
USER energy term |
| cmap |
1 |
CMAP energy term |
| |
| echeck |
20.0 |
energy tolerance check for dynamics |
| |
| ace |
0 |
ACE implicit solvation |
| aceieps |
1.0 |
ACE internal dielectric |
| aceseps |
80.0 |
ACE external dielectric |
| acealpha |
1.3 |
ACE alpha |
| acesigma |
undef |
ACE sigma |
| acevscale |
1.0 |
ACE volume scale |
| |
| sasagamma |
0.00542 |
gamma for SASA |
| sasadelta |
0.920 |
delta for SASA |
| |
| gb |
undef |
Generalized Born implicit solvent: bgb, gbmf, gbmf2, gbmva, gbmvg |
| gbeps |
80.0 |
epsilon in GB prefactor |
| |
| gbcrad |
0.91 |
BGB radius scaling of main chain carbon w/ param19 |
| gbhrad |
0.8 |
BGB radius scaling of hydrogen atoms w/ param22 |
| gblambda |
undef |
BGB lambda factor |
| |
| gbmvad |
undef |
GBMVA shift |
| gbmvade |
undef |
GBMVA eshift |
| gbmvas |
undef |
GBMVA slope |
| gbmval1 |
0.5 |
GBMVA lambda 1 |
| gbmvap1 |
0.45 |
GBMVA P1 |
| gbmvap2 |
1.25 |
GBMVA P2 |
| gbmvap3 |
0.65 |
GBMVA P3 (old: 0.70) |
| gbmvap4 |
undef |
GBMVA P4 |
| gbmvap5 |
undef |
GBMVA P5 |
| gbmvap6 |
8.0 |
GBMVA P6, Still's factor |
| gbmvap7 |
undef |
GBMVA P7, VSA adjustment |
| gbmvaig |
32 |
GBMVA integration grid size |
| gbmvafrq |
undef |
GBMVA alpha update frequency |
| gbmvdrfrq |
undef |
GBMVA surface integration point update frequency |
| gbmvaimp |
undef |
GBMVA impulse derivatives |
| gbmvaemp |
undef |
GBMVA exponentially damped impulse |
| gbmvarith |
undef |
GBMVA arithmetic mean: alpha_ij = alpha_i+alpha_j |
| gbmvabuf |
0.2 |
GBMVA buffer for dynamics |
| gbmvabeta |
-12 |
GBMVA beta parameter (old: -20) |
| gbmvaonx |
1.9 |
GBMVA OnX parameter |
| gbmvaoffx |
2.1 |
GBMVA OffX parameter |
| gbmvacubic |
undef |
GBMVA cubic VSA |
| gbmvacorr |
1 |
GBMVA r7 correction (1) or r5 correction (0) |
| gbmvaextra |
undef |
GBMVA extra commands |
| gbmvagcut |
undef |
GBMVA GCUT (1 or 2) |
| gbmvakappa |
undef |
GBMVA kappa |
| gbmvafast |
undef |
GBMVA FAST |
| gbmvasgbfrq |
4 |
GBMVA SGBFRQ |
| gbmvasxd |
0.3 |
GBMVA SGBFRQ delta |
| |
| gbmva1 |
undef |
GBMV A1 parameter |
| gbmva2 |
undef |
GBMV A2 parameter |
| gbmva3 |
undef |
GBMV A3 parameter |
| gbmva4 |
undef |
GBMV A4 parameter |
| gbmva5 |
undef |
GBMV A5 parameter |
| gbmvdf |
undef |
GBMV adjustment factor for shift |
| gbmvdoff |
undef |
GBMV epsilon offset for shift adjustment |
| gbmvmstl |
undef |
GBMV modified Still |
| gbmvms0 |
1.0 |
GBMV MS0 parameter |
| gbmvms1 |
0.0 |
GBMV MS1 parameter |
| gbmvms2 |
0.0 |
GBMV MS2 parameter |
| gbmvms3 |
0.0 |
GBMV MS3 parameter |
| |
| gbmvdefmnp |
0 |
turn on default membrane non-polar profile |
| gbmvzs |
0.5 |
parameters for membrane non-polar profile |
| gbmvzm |
9.2 |
parameters for membrane non-polar profile |
| gbmvzt |
25 |
parameters for membrane non-polar profile |
| gbmvst |
0.32 |
parameters for membrane non-polar profile |
| |
| gbmveps |
undef |
GBMV solvent dielectric |
| gbmvepsu |
undef |
GBMV solute ref dielectric |
| |
| gbmvdu |
undef |
GBMV adj. delta for solute dielectric |
| |
| gbmvsa |
0.015 |
GBMV hydrophobic SASA term factor |
| gbmvsb |
0.900 |
GBMV hydrophobic SASA term offset |
| gbmvsagb |
undef |
GBMV hydrophobic SASA term on a selection basis |
| |
| gbmvason |
1.2 |
GBMV SASA internal parameter, old: 0.5 |
| gbmvasoff |
1.5 |
GBMV SASA internal parameter, old: 1.75 |
| |
| gbswsw |
0.3 |
GBSW switching length |
| gbswrmax |
20.0 |
GBSW maximum integration radius |
| gbswnang |
38 |
GBSW number of angular integration points |
| gbswnrad |
0 |
GBSW number of radial integration points |
| gbswsgamma |
0.00 |
GBSW surface tension coefficient |
| gbswdgp |
1.5 |
GBSW grid spacing for lookup table |
| gbswrbuffer |
0.0 |
GBSW buffer region for lookup table |
| gbswtmemb |
0.0 |
GBSW thickness of membrane |
| gbswmsw |
0.3 |
GBSW membrane switching length |
| gbswms |
0 |
GBSW molecular surface approx. |
| |
| hdgbprofile |
undef |
epsilon profile for HDGB |
| hdgbnpprofile |
undef |
non-polar profile for HDGB |
| |
| scalerad |
0 |
scaled radii for GB/PB |
| |
| dcel |
0.5 |
PB grid spacing |
| epsw |
80.0 |
epsilon for solvent |
| epsp |
1.0 |
epsilon for solute |
| epspr |
undef |
epsilon for solute reference if set |
| epsr |
1.0 |
epsilon for reference environment |
| smooth |
0 |
smooth boundary |
| pbdelta |
8.0 |
distance to boundary |
| proberad |
1.4 |
water probe radius |
| pbionr |
2.0 |
ion exclusion radius |
| pbionconc |
0.0 |
ion concentration |
| pbtemp |
300.0 |
temperature |
| pbextra |
"" |
extra parameters for PBEQ |
| |
| chargefile |
undef |
load charges from external file |
| |
| volumespace |
200000 |
space for volume calculation |
| rdfrmax |
undef |
maximum radius for RDF analysis |
| rdfbins |
100 |
number of bins for RDF analysis |
| rdfspfac |
10 |
space allocation for RDF analysis |
| rdfvolume |
undef |
normalization volume for RDF analysis |
| rdfexclude |
undef |
bygr, byres, byseg to exclude self pairs |
| diffrange |
undef |
distance range for diffusion calculation |
| puckermode |
"AS" |
AS or CP pucker calculation |
| |
| sradfac |
1.0 |
overall scaling factor for GB/PB radii |
| sbackn |
1.0, # 0.90 |
peptide backbone N scaling factor |
| sbacko |
1.0, # 0.94 |
peptide backbone O scaling factor |
| sbackca |
1.0 |
peptide backbone CA scaling factor |
| |
| mfnh |
undef |
radius for H* |
| mfn3 |
undef |
radius for ch3 |
| mfn2 |
undef |
radius for cb |
| mfnb10 |
undef |
radius for backbone CA (GLY) |
| mfnb9 |
undef |
radius for backbone CA |
| mfnb6 |
undef |
radius for backbone C |
| mfnb7 |
undef |
radius for backbone O |
| mfnb8 |
undef |
radius for backbone N |
| mfn5 |
undef |
radius for ch |
| mfn13 |
undef |
radius for roh |
| |
| mfn4 |
undef |
radius for cet |
| mfn19 |
undef |
radius for crh |
| mfn18 |
undef |
radius for cpro |
| mfn7 |
undef |
radius for ctrp |
| mfn16 |
undef |
radius for ntrp |
| mfn8 |
undef |
radius for css |
| mfn17 |
undef |
radius for sulfur |
| mfn25 |
undef |
radius for s2 |
| mfn6 |
undef |
radius for cam |
| mfn15 |
undef |
radius for nam |
| mfn11 |
undef |
radius for oam |
| mfn10 |
undef |
radius for ocar |
| mfn9 |
undef |
radius for cze |
| mfn14 |
undef |
radius for nal |
| mfn21 |
undef |
radius for nhis |
| |
| nina9 |
undef |
radius for ARG CZ |
| nina9l |
undef |
radius for LYS CE |
| nina10 |
undef |
radius for GLU/ASP OE*/OD* |
| nina11 |
undef |
radius for ASN/GLN OE*/OD* |
| nina14 |
undef |
radius for ARG NH*/NE |
| nina14l |
undef |
radisu for LYS NZ |
| nina7 |
undef |
radius for TRP CE*/CD*/CZ*/CH2 |
| nina16 |
undef |
radius for TRP NE1 |
| |
| nina3 |
undef |
radius for CG* |
| ninah |
undef |
radius for H* |
| ninab1 |
undef |
radius for backbone CAY/CAT |
| ninab2 |
undef |
radius for backbone CY |
| ninab3 |
undef |
radius for backbone OY |
| ninab4 |
undef |
radius for backbone NT |
| ninab5 |
undef |
radius for backbone OT* |
| ninab6 |
undef |
radius for backbone C |
| ninab7 |
undef |
radius for backbone O |
| ninab8 |
undef |
radius for backbone N |
| ninab9 |
undef |
radius for backbone CA |
| ninab10 |
undef |
radius for backbone CA (GLY) |
| nina2 |
undef |
radius for CB |
| nina4 |
undef |
radius for GLU CG |
| nina5 |
undef |
radius for CD* |
| nina6 |
undef |
radius for GLN CD/ASN CG/GLU CD/ASP CG |
| nina18 |
undef |
radius for PRO GB/CG/CD |
| nina19 |
undef |
radius for TYR/PHE CE*/CD*/CZ |
| nina8 |
undef |
radius for MET CE |
| nina20 |
undef |
radius for HSD CE1/HSD CD2 |
| nina13 |
undef |
radius for TYR OH |
| nina21 |
undef |
radius for HSD NE2/ND1 |
| nina22 |
undef |
radius for HSP NE2/ND1 |
| nina15 |
undef |
radius for GLN NE2/ASN ND2 |
| nina17 |
undef |
radius for S* |
| |
| asp |
0 |
flag to switch on ASP energy terms |
| aspfile |
undef |
external input file for ASP energy term |
| aspval |
5.42 |
ASP solvation parameter |
| aspvalc |
undef |
ASP solvation parameter for carbon atoms |
| aspvaln |
undef |
ASP solvation parameter for nitrogen atoms |
| aspvalo |
undef |
ASP solvation parameter for oxygen atoms |
| aspvalh |
undef |
ASP solvation parameter for hydrogen atoms |
| aspvals |
undef |
ASP solvation parameter for sulphur atoms |
| aspradh |
undef |
ASP hydrogen radius |
| aspref |
0.0 |
ASP reference area |
| |
| og |
0 |
flag to switch on Olgun's energy score |
| |
| eef1 |
0 |
flag to switch on EEF1 energy terms |
| eef1file |
"solvpar.inp" |
EEF1 parameter file |
| |
| sasa |
0 |
flag to switch on SASA energy terms |
| sasaeps |
2.0 |
SASA dielectric constant |
| sasasig1 |
-0.060 |
SASA sig 1 value |
| sasasig2 |
0.012 |
SASA sig 2 value |
| sasasig3 |
0.00 |
SASA sig 3 value |
| |
| sdsteps |
50 |
number of minimization steps for steepest descent min. |
| sdstepsz |
0.005 |
initial step size for steepest descent min. |
| updnbsd |
-1 |
update freq. for non-bonded list in steepest descent min. |
| |
| minmode |
"abnr" |
minimization protocol |
| minsteps |
500 |
number of minimization steps for min. |
| minstepsz |
0.005 |
initial step size for min. |
| minetol |
1.0E-5 |
energy tolerance for min. |
| minupdnb |
-1 |
update freq. for non-bonded list in min. |
| minoutfrq |
10 |
output freq. for minimization runs |
| |
| shake |
0 |
use shake |
| shaketol |
1.0E-8 |
shake tolerance |
| shakemode |
'hyd' |
'hyd'rogen or 'all' atoms are restrained |
| shakefast |
0 |
use fast vector/parallel version of shake |
| |
| periodic |
undef |
use periodic boundaries |
| explicit |
1 |
do not use implicit solvent for explicit solvent |
| solvent |
undef |
residue names of solvent molecules for PBC |
| imbyseg |
undef |
residue images by segment |
| imbyres |
undef |
residue images by residue |
| ewald |
1 |
use Ewald for explicit solvent |
| pmekappa |
undef, #0.32 |
PME distribution width |
| pmekmax |
5.0, #5.0 |
PME K max |
| npme |
undef, #64 |
number of grid points for PME grid |
| npmex |
undef |
number of grid points in x direction |
| npmey |
undef |
number of grid points in y direction |
| npmez |
undef |
number of grid points in z direction |
| |
| boxshape |
undef |
box shape for periodic boundaries |
| boxsize |
undef |
box size |
| boxx |
undef |
box x dimension |
| boxy |
undef |
box y dimension |
| boxz |
undef |
box z dimension |
| |
| dynens |
'NVT' |
dynamics ensemble 'NVT', 'NPT', 'NPH', 'NVE' |
| dynber |
0 |
use Berendsen thermostat |
| dynbertc |
5.0 |
coupling constant for Berendsen |
| dynnose |
undef |
use Nose-Hoover thermostat |
| dynnoseq |
50.0 |
Nose-Hoover qref |
| dynnosen |
5 |
Nose-Hoover ncyc |
| dyntstep |
0.002 |
dynamics time step in picoseconds |
| dynsteps |
100 |
dynamics steps |
| dyntemp |
298 |
dynamics temperature |
| dynitemp |
undef |
initial temperature for heating/equilibration |
| dynseed |
undef |
dynamics random seed |
| dyndeltat |
10.0 |
temperature change during heating/cooling |
| dynhtfrq |
-1 |
temperature change frequency |
| dyntrfrq |
undef |
trans/rot removal frequency |
| dyneqfrq |
200 |
equilibration frequency |
| dyntwin |
5.0 |
temperature window during equilibrition |
| dynscale |
undef |
temperature scaling factor for restarts |
| dynoutfrq |
undef |
frequency of energy/trajectory output |
| dynupdnb |
-1 |
update of non-bonded list |
| dynupdimg |
-1 |
update of images |
| dynpress |
1.00 |
the pressure (in atm) for NPT simulations |
| dynpgamma |
25.0 |
gamma value for NPT simulations |
| dynpmass |
400.0 |
Langevin piston mass for NPT simulations |
| dynpext |
0 |
Use external virial in NPT simulations |
| nblisttype |
"bycb" |
non-bonded list generation |
| dyncons |
undef |
KDYN dynamics |
| dynkmas |
0.1 |
KDYN dynamics mass |
| dynkfkc |
undef |
KDYN FKC |
| dynkdkc |
undef |
KDYN DKC |
| |
| phmd |
0 |
PHMD |
| phmdpar |
undef |
PHMD parameter file |
| phmdph |
7.0 |
simulation pH |
| phmdpri |
1000 |
print output file every 1000 steps |
| phmdmass |
10.0 |
mass for the titration and tautomer interconversion coordinates |
| phmdbarr |
2.5 |
titration barrier |
| phmdbartau |
2.5 |
tautomer interconversion barrier |
| phmdtemp |
298 |
PHMD temperature |
| phmdout |
"final.lamb" |
output file of lambda values |
| phmdderi |
undef |
compute derivatives |
| phmdtheta |
undef |
theta value if phmdderi defined |
| phmdthetax |
undef |
thetax value if phmdderi defined |
| phmdsel |
undef |
selection of titrating residues |
| |
| sgmd |
0 |
self-guided MD |
| sgmddrag |
0.2 |
SGMD drag force |
| sgmdavg |
1.0 |
SGMD average? |
| sgmdvfb |
-1.0 |
SGMD ? |
| sgmdfrq |
1 |
SGMD update frequency |
| |
| sgld |
0 |
self-guided Langevin dynamics |
| sgldtsvg |
0.2 |
local avg time |
| sgldtsvp |
10 |
guiding effect avg time |
| sgldtpsg |
1.0 |
giding temperature |
| sgldsgft |
0.0 |
guiding factor |
| sgldsgmv |
0 |
allow guiding force on center of mass |
| sgldistr |
1 |
index of the first atom for guiding force application |
| sgldiend |
"natom" |
index of the last atom for guiding force application |
| |
| noerest |
undef |
file name with NOE restraint commands |
| xnoerest |
undef |
X-plor file name with NOE restraint commands |
| noerexp |
3 |
exponent for distance averaging |
| noekmin |
1.0 |
force constant for small distance harmonic potential |
| noekmax |
1.0 |
force constant for large distance harmonic potential |
| noefmax |
9999.0 |
maximum force |
| noescale |
1.0 |
overall scaling factor |
| |
| nlambda |
10 |
number of windows for PERT sampling |
| pequi |
1000 |
number of equilibration steps |
| pprod |
4000 |
number of production steps |
| ilambda |
undef |
run individual lambda step (0 .. nlambda) |
| |
| #qfep |
0 |
charging FEP |
| #qfepfix |
1 |
fix segment |
| #qfepsel |
"segid PRO0" |
selection for charging FEP |
| |
| dynextra |
undef |
extra dynamics command |
| |
| qcor |
undef |
Ewald charge correction |
| whamtol |
0.001 |
WHAM tolerance |
| whamsteps |
200 |
WHAM iteration steps |
| whammaxtime |
1000000 |
WHAM maximum time |
| whammaxwin |
200 |
WHAM maximum number of windows |
| |
| dyntp |
undef |
turn on TP control |
| dyntpcmda |
0 |
TPControl dampening of center of mass motion |
| dyntptau |
0.05 |
characteristic thermostat response time in ps |
| dyntppress |
1.0 |
set reference pressure |
| dyntpbtau |
0.05 |
characteristic barostat response time in ps |
| |
| lang |
0 |
flag for running Langevin dynamics |
| langrbuf |
0.0 |
radius of Langevin inner buffer sphere |
| langfbeta |
5.0 |
friction coefficient for Langevin dynamics |
| langsel |
undef |
CHARMM atom selection to apply Langevin friction |
| langfile |
undef |
file for setting friction coefficients |
| |
| |
