From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Tue Nov 20 2007 - 16:07:01 CST
Dear Vaithee,
Thanks for your message, this is a mistake in the documentation. The
list of 4 atom indices should be passed through the parameter abf1:
abf abf1 "4 5 1 2"
Best,
Jerome
On Nov 20, 2007 4:56 PM, Subramanian Vaitheeswaran <vaithee_at_umd.edu> wrote:
> Dear ABF and NAMD developers,
>
> I downloaded the files dihedral.tcl and dihedral-com.tcl into ~/NAMD_2.6_Linux-i686/lib/abf from the ABF website. Do I need to do any thing else to use these new order parameters?
>
> When I run a test job with "abf coordinate dihedral", it dies with the error:
> TCL: Unknown ABF keyword: abf3
> FATAL ERROR: Unknown ABF keyword: abf3.
>
> Here is the ABF part of my conf file:
> #######################################################
> ## ABF ##
> #######################################################
> if {1} {
> source ~/NAMD_2.6_Linux-i686/lib/abf/abf.tcl
> abf coordinate dihedral
> abf abf1 {6}
> abf abf2 {8}
> abf abf3 {14}
> abf abf4 {16}
> abf dxi 0.1
> abf xiMin 0.1
> abf xiMax 179.9
> abf outFile abf_AA.pmf
> abf historyFile abf_AA.hist
> abf fullSamples 200
> abf inFiles {}
> abf dSmooth 0.0
> abf restraintList {}
> #######################################################
> Any help in fixing this problem is much appreciated.
>
> thanks,
> Vaithee
>
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