problems NAMD_2.6 (fwd)

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:19:02 CST