Re: Free energy calculation fixing the dihedrals

From: Luca Bellucci (bellucci14_at_unisi.it)
Date: Tue Nov 25 2008 - 02:48:06 CST

Hi Jogan,
you have a problem with dihedral angle input.
You can try with
abf1 { 768 445 2009 2332 }

Luca

> Hello,
> 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
> "ABFcoord"
> (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
> "calcforces"
>
> 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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