VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 29 2021 - 10:25:00 CDT

Hi,
  You'll get much better responses to your questions by posting
NAMD questions on the NAMD-L mailing list. VMD-L is intended for
VMD related questions. The errors you're seeing from NAMD look to
me like basic syntax errors that exist in one or more of your configuration
files/scripts. You mention that it's the same script that you're running
on a different computer, so I would also compare them with "diff" and make
sure that one of them didn't get corrupted somehow.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 29, 2021 at 05:22:39PM +0530, SYEDA SABIHA SULTANA LUBNA . wrote:
> Hi,
> Can someone help me in understanding why I am getting this error message?
> This is when i am trying to run my FEP calculation on centose 8 version.
> where as the same script is working on ubuntu 20 version.
> Info: Based on Charm++/Converse 61002 for
> charmpp-6.10.2-rcdhh4jp7pfjtdz5hragsqhs5elcvieh
> Info: Built Mon Jan 11 20:27:40 IST 2021 by root on sharanga
> Info: 1 NAMD  2.14  linux-x86_64-netlrts  64   node4  2032
> Info: Running on 64 processors, 1 nodes, 1 physical nodes.
> Info: CPU topology information available.
> Info: Charm++/Converse parallel runtime startup completed at 0.0428052 s
> CkLoopLib is used in SMP with simple dynamic scheduling (converse-level
> notification)
> Info: 4681.57 MB of memory in use based on /proc/self/stat
> Info: Configuration file is rest-01.namd
> Info: Working in the current directory /home/debashreeb/FEP_complex
> Info: Sourcing fep.tcl
> Warning: Couldn't parse line 105 in configuration file fep.tcl. The line
> was: Â Â }
> Warning: Couldn't parse line 117 in configuration file fep.tcl. The line
> was: Â Â Â }
> Warning: Couldn't parse line 124 in configuration file fep.tcl. The line
> was: Â Â }
> Warning: Couldn't parse line 137 in configuration file fep.tcl. The line
> was: Â Â }
> Warning: Couldn't parse line 138 in configuration file fep.tcl. The line
> was: }
> Warning: Couldn't parse line 238 in configuration file fep.tcl. The line
> was: Â Â }
> Warning: Couldn't parse line 246 in configuration file fep.tcl. The line
> was: Â Â }
> Warning: Couldn't parse line 247 in configuration file fep.tcl. The line
> was: }
> Warning: Couldn't parse line 258 in configuration file fep.tcl. The line
> was: Â Â }
> Warning: Couldn't parse line 271 in configuration file fep.tcl. The line
> was: Â Â Â Â }
> Warning: Couldn't parse line 276 in configuration file fep.tcl. The line
> was: Â Â Â Â }
> Warning: Couldn't parse line 277 in configuration file fep.tcl. The line
> was: Â Â Â }
> Warning: Couldn't parse line 278 in configuration file fep.tcl. The line
> was: Â Â }
> Warning: Couldn't parse line 281 in configuration file fep.tcl. The line
> was: }
> Warning: Couldn't parse line 294 in configuration file fep.tcl. The line
> was: Â Â }
> Warning: Couldn't parse line 297 in configuration file fep.tcl. The line
> was: Â Â }
> Warning: Couldn't parse line 299 in configuration file fep.tcl. The line
> was: }
> ERROR: Expecting value and optional units for option 'langevinTemp'
> ERROR: Multiple definitions of 'alchLambda'
> ERROR: Â in the configuration file are not allowed
> ERROR: Expecting value and optional units for option 'alchLambda'
> ERROR: Multiple definitions of 'alchLambda2'
> ERROR: Â in the configuration file are not allowed
> ERROR: Expecting value and optional units for option 'alchLambda2'
> ERROR: Multiple definitions of 'alchLambdaIDWS'
> ERROR: Â in the configuration file are not allowed
> ERROR: Expecting value and optional units for option 'alchLambdaIDWS'
> ERROR: Expecting value and optional units for option 'LangevinPistonTemp'
> ERROR: 'LangevinPistonTemp' was set to 0 but it should be positive
> ERROR: Multiple definitions of 'firsttimestep'
> ERROR: Â in the configuration file are not allowed
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR: Â Â runFEP
> ERROR: Â Â runTIlist
> ERROR: Â Â reinitvels
> ERROR: Â Â minimize
> ERROR: Â Â return
> ERROR: Â Â lappend
> ERROR: Â Â while
> ERROR: Â Â }
> ERROR: Â Â runFEPlist
> ERROR: Â Â incr
> ERROR: Â Â run
> ERROR: Â Â $win
> ERROR: Â Â print
> ERROR: Â Â foreach
> ERROR: Â Â if
> Thanks for the help.
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-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/