Re: Trouble in fep.tcl file for FEP run in NAMD

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Nov 02 2021 - 06:33:41 CDT

Hi,

Can you double-check that fep.tcl is identical to the one shipped with NAMD?

Also, try removing the line "source fep.tcl" and see if any syntax error shows up, besides the missing alchemical parameters.

Jerome

----- On 30 Oct 21, at 9:02, SYEDA SABIHA SULTANA LUBNA . <p20190061_at_hyderabad.bits-pilani.ac.in> 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: }
> Warning: Couldn't parse line 117 in configuration file fep.tcl. The line was: }
> Warning: Couldn't parse line 124 in configuration file fep.tcl. The line was: }
> Warning: Couldn't parse line 137 in configuration file fep.tcl. The line was: }
> 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: }
> Warning: Couldn't parse line 246 in configuration file fep.tcl. The line was: }
> 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: }
> Warning: Couldn't parse line 271 in configuration file fep.tcl. The line was: }
> Warning: Couldn't parse line 276 in configuration file fep.tcl. The line was: }
> Warning: Couldn't parse line 277 in configuration file fep.tcl. The line was: }
> Warning: Couldn't parse line 278 in configuration file fep.tcl. The line was: }
> 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: }
> Warning: Couldn't parse line 297 in configuration file fep.tcl. The line was: }
> 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: in the configuration file are not allowed
> ERROR: Expecting value and optional units for option 'alchLambda'
> ERROR: Multiple definitions of 'alchLambda2'
> ERROR: in the configuration file are not allowed
> ERROR: Expecting value and optional units for option 'alchLambda2'
> ERROR: Multiple definitions of 'alchLambdaIDWS'
> ERROR: 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: in the configuration file are not allowed
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR: runFEP
> ERROR: runTIlist
> ERROR: reinitvels
> ERROR: minimize
> ERROR: return
> ERROR: lappend
> ERROR: while
> ERROR: }
> ERROR: runFEPlist
> ERROR: incr
> ERROR: run
> ERROR: $win
> ERROR: print
> ERROR: foreach
> ERROR: if

> Thanks for the help.

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