problem with paramters?

From: Albert (mailmd2011_at_gmail.com)
Date: Thu Mar 22 2012 - 00:25:27 CDT

hello:

   I've generated a membrane system by CHARMM-GUI. and I am trying to
run the following protocol:

/#############################################################
## JOB DESCRIPTION ##
#############################################################

# Min. and Eq. of protein
# embedded in POPC membrane, ions and water.
# Melting lipid tails. PME, Constant Volume.

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure ../step5_assembly.xplor.psf
coordinates ../step5_assembly.pdb
outputName popcwimineq-01

set temperature 310

# Continuing a job from the restart files
if {0} {
set inputname assembly
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
extendedSystem $inputname.restart.xsc
}

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ../toppar/par_all22_prot.prm;
parameters ../toppar/par_all27_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_all36_lipid_cholesterol.str;

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature

# Periodic Boundary conditions. Need this since for a start...
cellBasisVector1 76.6 0.0 0.0; # vector to the next image
cellBasisVector2 0.0 76.6 0.0;
cellBasisVector3 0.0 0.0 105.4;
cellOrigin 0.0 0.0 0.0; # the *center* of the cell

wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
wrapNearest off; # use for non-rectangular cells
(wrap to the nearest image)

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 80
PMEGridSizeY 80
PMEGridSizeZ 90
}

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}

restartfreq 1000 ;# 1000steps = every 2ps
dcdfreq 1000
xstFreq 1000
outputEnergies 50
outputPressure 50

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {1} {
fixedAtoms on
fixedAtomsFile ../fix_prot.pdb
fixedAtomsCol B
fixedAtomsForces on
}

#############################################################
## EXTRA PARAMETERS ##
#############################################################

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
if {1} {
minimize 1000
reinitvels $temperature
}

run 500000 ;# 0.5 ns
/

by command

namd2 +p24 eq6.1.inp>log &

It said:

/apo-s1p/work% ------------- Processor 0 Exiting: Called CmiAbort
------------
Reason: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
./toppar/toppar_water_ions.str
LINE=*set nat ?NATC*

Charm++ fatal error: / /
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
./toppar/toppar_water_ions.str
LINE=*set nat ?NATC* /

Then I try to use the following paramters:

/# Input
paraTypeCharmm on
parameters ../toppar/par_all22_prot.prm;
parameters ../toppar/par_all27_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_all36_lipid_cholesterol.str;
/
it said:

/apo-s1p/work% ------------- Processor 0 Exiting: Called CmiAbort
------------
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT
Charm++ fatal error:
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT /

does anybody have any idea what happen?

thank you very much

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:21 CST