From: Seke Keretsu (sekekeretsu_at_gmail.com)
Date: Wed Feb 03 2021 - 02:51:29 CST
Dear Experts,
I am posting this again as follow up to my previous post. Since then, I
followed and tried all the advice but the error was not resolved.
I am using NAMD2.14 for a protein ligand complex in which there is a lone
pair on the chlorobenzene of the ligand. The psf files were built in
Charmm-Gui and solvated and ionized with VMD 1.9.4.
As suggested, I have added 'lonepairs on' to the configuration file.
In the psf file (ionized.psf), I added the lines for the one lone pair as
advised (by Pang, Yui Tik):
1 3 !NUMLP NUMLPH
2 1 F 1.64000 0.00000 0.00000
4737 4710 4697
Here in the second line, I have tried 1.64 and -1.64 for distance between
lonepair and host. For polarized water it was negative, why?
In the third line, 4737 4710 4697 are the atomic ID of lonepair,
host and atom connected to host.
I still get the error as shown below regardless of the temperature I use.
*ERROR MESSAGE:*
ENERGY: 50020 287.8329 875.2009 2562.5041 35.3830
-139424.9435 155009.5692 0.0000 0.0000
0.0000 19345.5467 0.0000 19345.5467 19345.5467
0.0000 123095.5120 107654.6219 396330.9410 123095.5120
107654.6219
TCL: Running for 500000 steps
ERROR: Margin is too small for 1 atom during timestep 50026.
ERROR: Incorrect nonbonded forces and energies may be calculated!
ERROR: Atom 4737 velocity is -2369.83 -18252.9 -15708.5 (limit is 12000,
atom 395 of 507 on patch 37 pe 0)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
patch 37 pe 0).
FATAL ERROR: Exiting prematurely; see error messages above.
As suggested (by Laurent Chaloin), I have also checked the content of
"par_all36_cgenff.prm." Since I am using NAMD for simulation I assume the
lines should not be comment-out.
LPH CLGR1 0.00 0.0000 ! aromatic halogen to lone pair
LPH BRGR1 0.00 0.0000 ! aromatic halogen to lone pair
LPH IGR1 0.00 0.0000 ! aromatic halogen to lone pair
However I could not find the following lines in my .prm file. I tried
running a few times by appending the lines to my par_all36_cgenff.prm file.
Did not change the outcome.
Please advise if I missed something here. Also, Is there an alternative to
this, such as building a system without a lone pair without badly
compromising my simulation protocol ?
Thank you.
Seke
CONFIGURATION FILE:
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ionized.psf
coordinates ionized.pdb
set temperature 100
set outputname equilibration02
firsttimestep 50000
bincoordinates equilibration.restart.coor
#binvelocities equilibration.restart.vel
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters jz4/jz4.prm
parameters toppar/par_all36_carb.prm
parameters toppar/par_all36_cgenff.prm
parameters toppar/par_all36_lipid.prm
parameters toppar/par_all36m_prot.prm
parameters toppar/par_all36_na.prm
parameters toppar/par_interface.prm
parameters toppar_water_ions.str
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Integrator Parameters
timestep 1.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 69.61299896240234 0 0
cellBasisVector2 0 76.30400085449219 0
cellBasisVector3 0 0 74.61400032043457
cellOrigin 12.257286071777344 7.4436726570129395 -19.06593894958496
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
#manual grid definition
#PMEGridSizeX 45
#PMEGridSizeY 45
#PMEGridSizeZ 48
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
constraints on
consexp 2
consref prot_posres.ref
conskfile prot_posres.ref
conskcol B
constraintScaling 10.0
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
lonepairs on
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 20 #system was minimized already
#reinitvels $temperature
run 500000 ;# 50ps
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