ERROR: Stray PME grid charges detected
Dear all,
I have a system protein+ligand in a water box plus Na+
ions to neutralise the system. I'm using amber imput files. I'm trying to minimize and then equilibrate water and ions with simulated annealing but
i'm having a lot of problem. the starting point was the minimized system protein+ligand. Then I made the imput files with amber (sander) then I
minimized again the system protein+ligand+boxwater+Na with namd for 100000steps, with periodic boundary conditions, PME anf fixed protein
backbone.
here you can find the config file:
--------------------------------------------------------------------------
amber
yes
parmfile M52SKIrespambermin.prmtop
ambercoor
M52SKIrespambermin.prmcrd
readexclusions off
outputname
1M52SKIrespsimulatedannealing
restartName 1m52SKIrespsimannrest
set temperature
0
# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart
file!
temperature $temperature
# Periodic Boundary conditions
# NOTE: Do not set the
periodic cell basis if you have also
# specified an .xsc restart file!
cellBasisVector1 87. 0.
0.
cellBasisVector2 0. 67 0.
cellBasisVector3 0.
0 91.
cellOrigin -0.34 0.01 0.13
wrapAll
on
# Force-Field Parameters
exclude
scaled1-4
1-4scaling 0.833333
cutoff
12.
switching on
switchdist
10.
pairlistdist 14.0
# Integrator Parameters
timestep
0.2;# 1 fs/step
numsteps 100000
rigidBonds
all ;# needed for 2fs steps
rigidTolerance 0.0005
nonbondedFreq
1
fullElectFrequency 2
stepspercycle 10
#PME (for full-system periodic
electrostatics)
PME
yes
PMEGridSizeX 90
PMEGridSizeY
90
PMEGridSizeZ 120
restartfreq
200 ;# 500steps = every 1ps
dcdfreq
100
outputEnergies 100
outputPressure
100
dcdfile 1m52SKIrespsimann.dcd
# Fixed Atoms Constraint (set PDB
beta-column to 1)
fixedAtoms on
fixedAtomsFile
fix.pdb
fixedAtomsCol B
minimization on
if {1}
{
minimize 100000
reinitvels
$temperature
}
------------------------------------------------------------
All run ok until the end and I visualized the
trajectory on vmd. From the biginning I have protein and ligand shifted at two opposite edge of the water box, almost all outside the
waterbox.
Then I wanted to run the simulated annealing steps, using restart files, here you can find config
file:
-------------------------------------------
amber
yes
parmfile M52SKIrespambermin.prmtop
ambercoor
M52SKIrespambermin.prmcrd
readexclusions off
outputname
1M52SKIrespMDsimulatedannealing
restartName 1m52SKIrespMDsimannrest
# Continuing a job from
the restart files
binCoordinates 1m52SKIrespsimannrest.coor
binVelocities
1m52SKIrespsimannrest.vel ;# remove the "temperature" entry if you use this!
extendedSystem
1m52SKIrespsimannrest.xsc
firsttimestep 100000
wrapAll
on
# Force-Field Parameters
exclude
scaled1-4
1-4scaling 0.833333
cutoff
12.
switching on
switchdist
10.
pairlistdist 14.0
# Integrator Parameters
timestep
1;# 1 fs/step
numsteps 11822000
rigidBonds
all ;# needed for 2fs steps
rigidTolerance 0.0005
nonbondedFreq
1
fullElectFrequency 2
stepspercycle 10
#PME (for full-system periodic
electrostatics)
PME
yes
PMEGridSizeX 90
PMEGridSizeY
90
PMEGridSizeZ 120
restartfreq
200 ;# 500steps = every 1ps
dcdfreq
100
outputEnergies 100
outputPressure
100
dcdfile 1m52SKIrespMDsimann.dcd
constraints
on
consRef restrain.pdb
consKFile
restrain.pdb
consKCol B
reassignFreq
1000
reassignTemp 0
minimize
1000
for { set TEMP 0 } {$TEMP<601} {incr TEMP 1} {
run 1000
reassignTemp $TEMP
}
run 500000
for
{ set TEMP 600 } {$TEMP>=300} {incr TEMP -1} {
reassignTemp $TEMP
run 1000
}
run 500000
run
4000000
--------------------------------------------------------------------
at the first step I have all energy values equal to
99999999.9999
after few minimization steps (50) I have warning message:
ERROR: Stray PME grid charges detected:
and:
Warning: Bad
global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
Warning: Stray PME grid charges
ignored!
at the end of minimization steps (1000)
when simulated annealing should start I have the error:
ERROR: Constraint
failure in RATTLE algorithm for atom 3433!
ERROR: Constraint failure; simulation has become unstable.
End of program
if I visualize
the trajectory file on vmd I can see protein and ligand at two opposite edge of the water box (as before) and some very long bond, not only with
hydrogen, but also C-N, or C-O.
How can I solve the problem? should I enlarge the periodic box or the PME dimension starting from the
minimization step?
Should I reduce the timestep?
thank you for your help
regards
Roberta
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: Wed Feb 29 2012 - 15:52:51 CST