Free energy calculation fixing the dihedrals

From: Jagan Mohan (
Date: Tue Nov 25 2008 - 01:12:10 CST

I am trying to do free energy calculation by altering a specific dihedral
using ABF calculation

My input file has the following lines in the end

 source ./abf.tcl
  abf coordinate dihedral
  abf abf0 {768}
  abf abf1 {445}
  abf abf2 {2009}
  abf abf3 {2332}
  abf ximin 5.0
  abf ximax -5.0
  abf dxi 0.1
  abf dsmooth 0.2
  abf forceconst 100.0
  abf fullsamples 1000
# abf infiles ${runnold}_${prefix}.abf
  abf outfile ${runn}_${prefix}.abf
  abf historyfile ${runn}_${prefix}.his
  abf outputfreq 50
  abf writexifreq 50
  abf distfile ${runn}_${prefix}.dis
  abf applyBias yes

I am getting the following error message on running NAMD

Reason: FATAL ERROR: can't read "coords(445)": no such element in array
    while executing
"getdihedral $coords($abf0) $coords($abf1) $coords($abf2) $coords($abf3)"
    (in namespace eval "::ABF::ABFcoord" script line 5)
    invoked from within
"namespace eval ABFcoord {
        loadcoords coords

        # unit : degrees (between -180 and 180)
        return [getdihedral $coords($abf0) $coords($abf1) $coords($abf..."
    (procedure "ABFcoord" line 3)
    invoked from within
    (in namespace eval "::ABF" script line 9)
    invoked from within
"namespace eval ::ABF {

# First timestep : we don't have forces
if { $timestep == 0 } {

        # must not be equal to $timestep - 1
        set timeStored -2
    (procedure "calcforces" line 2)
    invoked from within

Please help me out reagrding this... Do u also need me to attach abf.tcl,
abf_script.tcl and dihedral.tcl...

Thanks in advance

Jagan Mohan

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