Hello,

I am trying to run FEP simulations using NAMD VMD, yet am repeatedly faced with this error

FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE par_all36_carb.prm

LINE=*MASS -1 HCTIP3 1.00800 ! TIP3P water hydrogen*

When opening the file there are no asterisk before MASS and the line is not commented out. When that line is commented out, the next line provides the same error. Any thoughts?

This error wasn't seen when using the same parameter files for MD simulations.

Below is the script being used:

# Set parameters

set temperature 300 ;# Simulation temperature in Kelvin

set steps_per_run 5000 ;# Number of steps per lambda window

set total_runs 20 ;# Total number of lambda windows

set equilibration_runs 10 ;# Number of equilibration runs

set fep_file "fep_emp.fep" ;# FEP file describing the ligand decoupling

set outputname "outputEMP_FEP" ;# Prefix for output files

# Input files

structure

coordinates

paratypecharmm on

parameters par_all36_carb.prm

parameters par_all36_cgenff.prm

parameters par_all36_lipid.prm

parameters par_all36_na.prm

parameters par_all36m_pro.prm

parameters par_interface.prm

# Simulation setup

outputname $outputname

temperature $temperature

outputEnergies 1000

outputPressure 1000

outputTiming 1000

binaryoutput yes

restartfreq 5000

dcdfile $outputname.dcd

dcdfreq 1000

# Integrator parameters

timestep 1.0 ;# 2 fs time step for integration

rigidBonds none ;# Rigid bonds for hydrogen atoms

nonbondedFreq 1 ;# Non-bonded interactions frequency

fullElectFrequency 2 ;# Full electrostatics frequency

stepspercycle 20 ;# Number of steps per cycle

#Cutoff for non-bonded interactions

cutoff 12.0 ;# 12 or 10 A cutoff for non-bonded interactions

switching on ;# Enable switching function

switchDist 10.0 ;# Switching starts at 10 A

exclude 1-2 ;# Exclude interactions between 1-2 bonded atoms

# PME (Particle Mesh Ewald) parameters for electrostatics

PME on

PMEGridSizeX 109

PMEGridSizeY 109

PMEGridSizeZ 109

# Constraints

constraints off

# Temperature control

langevin on

langevinDamping 5

langevinTemp $temperature

langevinHydrogen off

# Pressure control

useGroupPressure yes

useFlexibleCell no

useConstantArea no

langevinPiston on

langevinPistonTarget 1.01325

langevinPistonPeriod 200.0

langevinPistonDecay 100.0

langevinPistonTemp $temperature

wrapAll on

# Initial minimization

minimize 1000

# Equilibration phase

for {set i 0} {$i < $equilibration_runs} {incr i} {

run $steps_per_run

}

# FEP calculation: Decoupling ligand from macromolecule

fep yes

fepFile $fep_file

fepColvars on

# Perturbation lambda schedule

lambda 0.0

for {set i 1} {$i