From: carles ferrer (gandalf_at_mmb.pcb.ub.es)
Date: Thu Sep 29 2005 - 04:06:09 CDT
-- Carles Ferrer-Costa PhD. tel +34934037155 Molecular Modelling and Bioinformatics fax +34934037157 IRBB-Parc Cientific de Barcelona. UB e-mail:gandalf_at_mmb.pcb.ub.es Josep Samitier, 1-5 08028 Barcelona. c.ferrer.costa_at_gmail.com ---------- Forwarded message ---------- Date: Wed, 21 Sep 2005 16:32:39 +0200 (CEST) From: carles ferrer <gandalf_at_mmb.pcb.ub.es> To: jim_at_ks.uiuc.edu, johns_at_ks.uiuc.edu Subject: problems NAMD_2.6 Dear Developers, I'm trying the new gromacs option in NAMD_2.6b1_Linux-i686 version downloaded directly from your home. surprisingly I've got this fatal error (shown above) runing the above also parameters file. I figured out that there is some problem reading this keyword in on because when running an amber or charmm in file with gromacs off option no problems appear. Any idea? Thanks in advance gandalf_at_pluto 195% /hosts/nd44/gandalf/NAMD/NAMD_2.6b1_Linux-i686/namd2 *.in Charm++: standalone mode (not using charmrun) Info: NAMD 2.6b1 for Linux-i686 Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: and send feedback or bug reports to namd_at_ks.uiuc.edu Info: Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999) Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 50900 for net-linux-iccstatic Info: Built Fri Jul 29 11:30:30 CDT 2005 by jim on kyoto.ks.uiuc.edu Info: Sending usage information to NAMD developers via UDP. Sent data is: Info: 1 NAMD 2.6b1 Linux-i686 1 pluto.mmb.pcb.ub.es gandalf Info: Running on 1 processors. Info: 7723 kB of memory in use. Info: Configuration file is 1kte_md001.in TCL: Suspending until startup complete. Info: Changed directory to /hosts/raid2/people/gandalf/CHARMM/PROVES/TMP/LOS28/TMP/GROMOS/1KTE/ FATAL ERROR: Please specify either XPLOR or CHARMM format for parameters! ------------- Processor 0 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: Please specify either XPLOR or CHARMM format for parameters! Charm++ fatal error: FATAL ERROR: Please specify either XPLOR or CHARMM format for parameters! runing this parameters file # NAMD conf file for MD simulation # 100 ps system without restraints # cte. pressure cwd /hosts/raid2/people/gandalf/CHARMM/PROVES/TMP/LOS28/TMP/GROMOS/1KTE/ gromacs on grotopfile 1kte.top grocoorfile 1kte.gro # # SHAKE to the bond between each hydrogen and its mother atom # only in H ntc 2 ntf 2 rigidBonds all rigidTolerance 0.0005 # Default is 0.00001 # # 100000 femtosecond = 100 picosecond numsteps 100000 firsttimestep 0 timestep 1 # in unit of fs cause shake only in H restartfreq 1000 # Restart file frequency DCDfreq 1000 # Trajectory file frequency DCDfile 1kte_md001dcd # trajectory filename outputEnergies 1000 # Energy output frequency # rescaletemp 300 # Do not needed any more after equilibration/Langevin # rescaleFreq 100 # Do not needed any more after equilibration/Langevin # # As in TB nonBondedFreq 2 fullElectFrequency 4 stepsPerCycle 20 # Default, increase parallel scalling # # Non-bonded cutoff 10 # pairlistdist 11 switching on # Turn on the switching functions switchdist 9 # distance where starts binaryoutput no # Turn off output in binary files binaryrestart no # Turn off restartt in binary files # # Temperature coupling langevin on # do langevin dynamics langevinDamping 5 # damping coefficient (gamma) of 5/ps (needed for SMD, just in case) langevinTemp 300 # bath temperature langevinHydrogen off # # Pressure coupling useGroupPressure yes # required with shake useFlexibleCell no #isotropic useConstantRatio no #isotropic langevinPiston on langevinPistonTarget 1.01325 # in bar -> 1 atm langevinPistonPeriod 200 langevinPistonDecay 100 langevinPistonTemp 300 # Recentering the box wrapAll on wrapNearest on PME on # Use PME for electrostatic calculation PMEGridSizeX 64 PMEGridSizeY 64 PMEGridSizeZ 64 # #molecular system #forcefield # # files de entrada # coordinates 1kte_md000rst.coor # velocities 1kte_md000rst.vel extendedSystem 1kte_md000rst.xsc #periodic cell parameters file outputname 1kte_md001out # Prefix of output files restartname 1kte_md001rst # Prefix for restarts exclude scaled1-4 1-4scaling 0.833333 # =1/1.2, default is 1.0 -- Carles Ferrer-Costa PhD. tel +34934037155 Molecular Modelling and Bioinformatics fax +34934037157 IRBB-Parc Cientific de Barcelona. UB e-mail:gandalf_at_mmb.pcb.ub.es Josep Samitier, 1-5 08028 Barcelona. c.ferrer.costa_at_gmail.com
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