From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Tue Feb 07 2017 - 17:43:40 CST
Hi everyone,
I'm trying to do a simulation in Amber and I'm getting an unspecified error:
Info: Configuration file is UNTW.conf
Info: Working in the current directory (my directory)
TCL: Suspending until startup complete.
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: Using
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
[0] Stack Traceback:
[0:0] _Z8NAMD_diePKc+0x9d [0x66b25d]
[0:1] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x66
[0xec5d46]
[0:2] _ZN9NamdState14configListInitEP10ConfigList+0x294 [0xd83e84]
[0:3] _ZN9ScriptTcl3runEv+0x24c [0xe879ec]
[0:4] main+0x482 [0x680b72]
[0:5] __libc_start_main+0xf5 [0x7f8e3a590b35]
[0:6] [0x5c0d49]
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM
0
with errorcode 1.
Any idea of what could be going on? This is my conf file:
#INPUT#
amber on
parmfile dnainwater.prmtop
ambercoor min.pdb
temperature 300
#FORCE-FIELD PARAMETERS#
exclude scaled1-4
1-4scaling 1.0
watermodel tip3
rigidBonds all
cutoff 9.0
switching off
pairlistdist 11.0
rigidTolerance 0.0000001
useSettle on
#PARTICLE-MESH EWALD#
PME on
PMEGridSpacing 1.0
#INTEGRATOR PARAMETERS#
timestep 2
firstTimestep 0
fullElectFrequency 2
nonbondedfreq 1
#OUTPUT#
outputName untwist
binaryoutput no
outputenergies 1000
outputtiming 1000
outputpressure 1000
binaryrestart no
dcdfile Untwist.dcd
dcdfreq 1000
XSTFreq 1000
restartfreq 1000
restartname Untwist.restart
velDCDfile Untwist.veldcd
velDCDfreq 1000
# Constant Temperature Control is on
langevin on
langevintemp 300
langevinHydrogen off
langevindamping 1
# Constant Pressure Control is off
usegrouppressure yes
useflexiblecell no
useConstantArea no
langevinpiston off
langevinpistontarget 1
langevinpistonperiod 200
langevinpistondecay 200
langevinpistontemp 300
#PERIODIC CELL#
cellBasisVector1 14.039997100830078 0 0
cellBasisVector2 0 18.21900177001953 0
cellBasisVector3 0 0 44.552001953125
cellOrigin 56.612491607666016 58.681888580322266 66.78993225097656
wrapAll on
#CONSTRAINTS#
constraints on
consref s1restraints.pdb
conskfile s1restraints.pdb
constraintScaling 2
consexp 2
conskcol O #here we impose the stretching
selectConstraints on
selectConstrX on
selectConstrY on
selectConstrZ off
rotConstraints off
movingConstraints on
movingConsVel 0 0 0.0125
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile s1restraints.pdb
fixedAtomsCol B #here we fix the positions
#SCRIPT
numsteps 10000
Thanks a lot!
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