Mismatch in atom number between psf and dcd files

From: Wintrode, Patrick (pwintrod_at_rx.umaryland.edu)
Date: Fri Sep 28 2018 - 10:04:11 CDT

I generated namd structure and input files using the CHARMM GUI. When I ran the equilibration, everything appeared to run normally. However, when I attempt to load the resulting dcd output in vmd, I get the following error:

Invalid number of atoms in coordinate file
Mismatch between existing molecule or structure file atom count and coordinate or trajectory atom count

I loaded the same psf file that was used in running the simulation, and the error results when I attempt to load the output dcd. Shouldn't the simulation have crashed if there was a mismatch in atom number between the psf and the trajectory? I tried regenerating the inpu files from the CHARMM GUI, and also tried using a different pdb of a structurally related protein but get the same error. I've used the CHARMM GUI in the past to set up namd simulations without any problems. Can someone suggest where I should start looking for the source of this error? The inp file used to run the simulation is below.


Patrick L. Wintrode

structure ../step3_pbcsetup.xplor.ext.psf
coordinates ../step3_pbcsetup_rotated.pdb
extendedSystem ../step3_pbcsetup_rotated.xsc

set temp 303.15;
set outputname step4_equilibration;

# read system values written by CHARMM (need to convert uppercases to lowercases)
exec tr "\[:upper:\]" "\[:lower:\]" < ../step3_pbcsetup.str | sed -e "s/ =//g" > step3_pbcsetup.namd.str
source step3_pbcsetup.namd.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 500; # 500 steps = every 1ps
dcdfreq 1000;
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 1000; # 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/toppar_water_ions.str
parameters toppar/toppar_dum_noble_gases.str
parameters toppar/toppar_all36_prot_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_na_nad_ppi.str
parameters toppar/toppar_all36_na_rna_modified.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_inositol.str
parameters toppar/toppar_all36_lipid_lps.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_pyrophosphate.str
parameters toppar/toppar_all36_lipid_sphingo.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_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

# These are specified by CHARMM
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 yes; # 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 10.0; # 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 16.0; # 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 2.0; # 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;

wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
wrapNearest on; # 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 no; # yes for anisotropic system like membrane
useConstantRatio no; # keeps the ratio of the unit cell in the x-y plane constant A=B

langevin on
langevinDamping 1.0
langevinTemp $temp
langevinHydrogen off

# constant pressure
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 50.0
langevinPistonDecay 25.0
langevinPistonTemp $temp

# planar restraint
colvars on
exec sed -e "s/\$bb/1.0/g" -e "s/\$sc/0.1/g" mdsetup_restraint.namd.col > restraints/$outputname.col
colvarsConfig restraints/$outputname.col

minimize 10000
numsteps 90000000
run 25000

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:25 CST