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D0.1.inp
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#For water only minimisation. First open step5 .pdd and .psf to do ctrbox.tcl and fix_protein.tcl as normal.
#Do not change PME info in this script or add new lines. Only use .SC.pdb and .SC.psf for input structurs, see below.
#Open the fix_protein.pdb change occupancy of IONS from 1.00 0.00 to 0.00 0.00 to make them mobile. This input uses
#NPT and constrains to minimise water + ions only. Run this and the run D0.2.inp
structure No_Nter_Gnrh_1_SC.psf
coordinates No_Nter_Gnrh_1_SC.pdb
set temp 300;
set outputname D0.1;
# read system values written by CHARMM (need to convert uppercases to lowercases)
exec tr "\[:upper:\]" "\[:lower:\]" < ../step5_assembly.str | sed -e "s/ =//g" > step5_input.str
source step5_input.str
temperature $temp;
outputName $outputname; # base name for output from this run
# NAMD writes two files at the end, final coord and vel
# in the format of first-dyn.coor and first-dyn.vel
firsttimestep 0; # last step of previous run
restartfreq 1000; # 1000 steps = every 2ps
dcdfreq 5000;
dcdUnitCell yes; # the file will contain unit cell info in the style of
# charmm dcd files. if yes, the dcd files will contain
# unit cell information in the style of charmm DCD files.
xstFreq 5000; # XSTFreq: control how often the extended systen configuration
# will be appended to the XST file
outputEnergies 125; # 125 steps = every 0.25ps
# The number of timesteps between each energy output of NAMD
outputTiming 1000; # The number of timesteps between each timing output shows
# time per step and time to completion
# Force-Field Parameters
paraTypeCharmm on; # We're using charmm type parameter file(s)
# multiple definitions may be used but only one file per definition
parameters toppar/par_all36m_prot.prm
parameters toppar/par_all36_na.prm
parameters toppar/par_all36_carb.prm
parameters toppar/par_all36_lipid.prm
parameters toppar/par_all36_cgenff.prm
parameters toppar/par_interface.prm
parameters toppar/toppar_all36_moreions.str
parameters toppar/toppar_all36_nano_lig.str
parameters toppar/toppar_all36_nano_lig_patch.str
parameters toppar/toppar_all36_synthetic_polymer.str
parameters toppar/toppar_all36_synthetic_polymer_patch.str
parameters toppar/toppar_all36_polymer_solvent.str
parameters toppar/toppar_water_ions.str
parameters toppar/toppar_dum_noble_gases.str
parameters toppar/toppar_ions_won.str
parameters toppar/cam.str
parameters toppar/toppar_all36_prot_arg0.str
parameters toppar/toppar_all36_prot_c36m_d_aminoacids.str
parameters toppar/toppar_all36_prot_fluoro_alkanes.str
parameters toppar/toppar_all36_prot_heme.str
parameters toppar/toppar_all36_prot_na_combined.str
parameters toppar/toppar_all36_prot_retinol.str
parameters toppar/toppar_all36_prot_model.str
parameters toppar/toppar_all36_prot_modify_res.str
parameters toppar/toppar_all36_na_nad_ppi.str
parameters toppar/toppar_all36_na_rna_modified.str
parameters toppar/toppar_all36_lipid_sphingo.str
parameters toppar/toppar_all36_lipid_archaeal.str
parameters toppar/toppar_all36_lipid_bacterial.str
parameters toppar/toppar_all36_lipid_cardiolipin.str
parameters toppar/toppar_all36_lipid_cholesterol.str
parameters toppar/toppar_all36_lipid_dag.str
parameters toppar/toppar_all36_lipid_inositol.str
parameters toppar/toppar_all36_lipid_lnp.str
parameters toppar/toppar_all36_lipid_lps.str
parameters toppar/toppar_all36_lipid_mycobacterial.str
parameters toppar/toppar_all36_lipid_miscellaneous.str
parameters toppar/toppar_all36_lipid_model.str
parameters toppar/toppar_all36_lipid_prot.str
parameters toppar/toppar_all36_lipid_tag.str
parameters toppar/toppar_all36_lipid_yeast.str
parameters toppar/toppar_all36_lipid_hmmm.str
parameters toppar/toppar_all36_lipid_detergent.str
parameters toppar/toppar_all36_lipid_ether.str
parameters toppar/toppar_all36_lipid_oxidized.str
parameters toppar/toppar_all36_carb_glycolipid.str
parameters toppar/toppar_all36_carb_glycopeptide.str
parameters toppar/toppar_all36_carb_imlab.str
parameters toppar/toppar_all36_label_spin.str
parameters toppar/toppar_all36_label_fluorophore.str
# Nonbonded Parameters
exclude scaled1-4 # non-bonded exclusion policy to use "none,1-2,1-3,1-4,or scaled1-4"
# 1-2: all atoms pairs that are bonded are going to be ignored
# 1-3: 3 consecutively bonded are excluded
# scaled1-4: include all the 1-3, and modified 1-4 interactions
# electrostatic scaled by 1-4scaling factor 1.0
# vdW special 1-4 parameters in charmm parameter file.
1-4scaling 1.0
switching on
vdwForceSwitching on; # New option for force-based switching of vdW
# if both switching and vdwForceSwitching are on CHARMM force
# switching is used for vdW forces.
# You have some freedom choosing the cutoff
cutoff 12.0; # may use smaller, maybe 10., with PME
switchdist 8.0; # cutoff - 2.
# switchdist - where you start to switch
# cutoff - where you stop accounting for nonbond interactions.
# correspondence in charmm:
# (cutnb,ctofnb,ctonnb = pairlistdist,cutoff,switchdist)
pairlistdist 14.0; # stores the all the pairs with in the distance it should be larger
# than cutoff( + 2.)
stepspercycle 20; # 20 redo pairlists every ten steps
pairlistsPerCycle 2; # 2 is the default
# cycle represents the number of steps between atom reassignments
# this means every 20/2=10 steps the pairlist will be updated
# Integrator Parameters
timestep 1.0; # fs/step
rigidBonds water; # Bound constraint all bonds involving H are fixed in length
nonbondedFreq 1; # nonbonded forces every step
fullElectFrequency 1; # PME every step
# Constant Temperature Control ONLY DURING EQUILB
reassignFreq 500; # reassignFreq: use this to reassign velocity every 500 steps
reassignTemp $temp;
# Periodic Boundary conditions. Need this since for a start...
if { $boxtype == "hexa" } {
set b [expr {$a / 2 * sqrt(3)}]
set d [expr {$a / 2}]
set wrapnearst on
} else {
set wrapnearst off
set d 0.0
}
cellBasisVector1 $a 0.0 0.0; # vector to the next image
cellBasisVector2 $d $b 0.0;
cellBasisVector3 0.0 0.0 $c;
cellOrigin 0.0 0.0 $zcen; # the *center* of the cell
wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
wrapNearest $wrapnearst; # use for non-rectangular cells (wrap to the nearest image)
# PME (for full-system periodic electrostatics)
PME yes;
PMEInterpOrder 6; # interpolation order (spline order 6 in charmm)
PMEGridSpacing 1.0; # maximum PME grid space / used to calculate grid size
# Pressure and volume control
useGroupPressure yes; # use a hydrogen-group based pseudo-molecular viral to calcualte pressure and
# has less fluctuation, is needed for rigid bonds (rigidBonds/SHAKE)
useFlexibleCell yes; # yes for anisotropic system like membrane
useConstantRatio yes; # keeps the ratio of the unit cell in the x-y plane constant A=B
langevin on
langevinDamping 5.0
langevinTemp $temp
langevinHydrogen off
# constant pressure
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 50.0
langevinPistonDecay 25.0
langevinPistonTemp $temp
constraints on
consexp 2
consref restraints/prot_posres.ref
conskfile restraints/prot_posres.ref
conskcol B
constraintScaling 10.0
# planar restraint
exec sed -e "s/Constant \$fc/Constant 5/g" step5_input.colvar.str > restraints/$outputname.col
colvars on
colvarsConfig restraints/$outputname.col
# dihedral restraint
exec sed -e "s/\$FC/500/g" restraints/dihe.txt > restraints/$outputname.dihe
extraBonds yes
extraBondsFile restraints/$outputname.dihe
fixedAtoms on
fixedAtomsFile fix_protein.pdb
fixedAtomsCol O
minimize 1000
run 100000