From: Seke Keretsu (sekekeretsu_at_gmail.com)
Date: Sun Dec 20 2020 - 20:24:37 CST
Dear expert,
I ran into this problem during my simulation but couldn't find a solution
on the mailing list. If already resolved in another discussion please
advise or direct me to the resource.
FATAL ERROR: can't read "boxtype": no such variable while executing
"if { $boxtype == "hexa" } {
set b [expr {$a / 2 * sqrt(3)}]
set d [expr {$a / 2}]
set wrapnearst on
The simulation continued to run after the error message. Kindly advise on
how to proceed. System was set up using charmm-gui server. My
configuration file is given below.
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*configuration.namd*
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structure step5_charmm2namd.psf
coordinates step5_charmm2namd.pdb
set temp 303.15;
set outputname step6.1_equilibration;
# read system values written by CHARMM (need to convert uppercases to
lowercases)
exec tr "\[:upper:\]" "\[:lower:\]" < ../step5_assembly.str | sed -e "s/
=//g" > step5_charmm2namd.str
source step5_charmm2namd.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 50000; # 1000 steps = every 2ps
dcdfreq 10000;
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 10000; # XSTFreq: control how often
the extended systen configuration
# will be appended to the XST
file
outputEnergies 10000; # 125 steps = every 0.25ps
# The number of timesteps
between each energy output of NAMD
outputTiming 10000; # 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 defi
timestep 1.0; # fs/step
rigidBonds all; # 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 1.0
langevinTemp $temp
langevinHydrogen off
constraints on
consexp 2
consref restraints/prot_posres.ref
conskfile restraints/prot_posres.ref
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Thank you.
Faithfully,
Seke
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