VMD-L Mailing List
From: SYEDA SABIHA SULTANA LUBNA . (p20190061_at_hyderabad.bits-pilani.ac.in)
Date: Sat Oct 30 2021 - 01:58:38 CDT
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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
> http://www.ks.uiuc.edu/Research/vmd/
>
-- The information contained in this electronic communication is intended solely for the individual(s) or entity to which it is addressed. It may contain proprietary, confidential and/or legally privileged information. Any review, retransmission, dissemination, printing, copying or other use of, or taking any action in reliance on the contents of this information by person(s) or entities other than the intended recipient is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us by responding to this email or telephone and immediately and permanently delete all copies of this message and any attachments from your system(s). The contents of this message do not necessarily represent the views or policies of BITS Pilani.
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