AW: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Feb 10 2017 - 05:34:40 CST

• Next message: Radak, Brian K: "RE: PSFgen failed to guess coordinate due to bad angle CD CG HG2"
• Previous message: The Cromicus Productions: "[NAMD] Obtain dynamical matrix away from equilibrium"
• In reply to: The Cromicus Productions: "Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Actually we use PDB since always with amber. It’s more likely that you had some unreadable characters in the lines that you changed now.

Norman Geist

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von The Cromicus Productions
Gesendet: Donnerstag, 9. Februar 2017 19:02
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Cc: NAMD list <namd-l_at_ks.uiuc.edu>
Betreff: Re: namd-l: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

Thanks for your reply! That doesn't change much, the main problem was that

namd doesn't like pbd files as input and I had to convert it to rst7 format.

On Wed, Feb 8, 2017 at 3:22 AM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:

I’m surprised that NAMD seems to be unable to give the wrong command. But I think first off all you should add semicolons if you have comment after commands:

conskcol O #here we impose the stretching

should be

conskcol O; #here we impose the stretching

Away from that I don’t see something wrong.

Norman Geist

Von: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> ] Im Auftrag von The Cromicus Productions
Gesendet: Mittwoch, 8. Februar 2017 00:44
An: NAMD list <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu> >
Betreff: namd-l: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

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!

• Next message: Radak, Brian K: "RE: PSFgen failed to guess coordinate due to bad angle CD CG HG2"
• Previous message: The Cromicus Productions: "[NAMD] Obtain dynamical matrix away from equilibrium"
• In reply to: The Cromicus Productions: "Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:06 CST