From: SYEDA SABIHA SULTANA LUBNA . (p20190061_at_hyderabad.bits-pilani.ac.in)
Date: Sat Oct 30 2021 - 01:58:38 CDT

ok, thank you.

On Fri, Oct 29, 2021 at 8:55 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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
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