From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Wed Nov 21 2007 - 09:59:37 CST
Dear Jerome and other ABF developers,
Another question, about dihedral-com.tcl this time. Following the ABF website, I identified the four groups of atoms defining the dihedral as:
abf abf1 {6 7}
abf abf2 {8 9}
abf abf3 {14 15}
abf abf4 {16 17 18 19 20}
in my input conf file. This dies with the error:
TCL: Unknown ABF keyword: abf3
FATAL ERROR: Unknown ABF keyword: abf3
It seems from dihedral-com.tcl that the group numbering should run from abf0-abf3 instead of 1-4, but this doesn't help either. Then it complains about:
TCL: Unknown ABF keyword: abf0
FATAL ERROR: Unknown ABF keyword: abf0
What is the correct usage?
thanks,
Vaithee
---- Original message ----
>Date: Tue, 20 Nov 2007 17:07:01 -0500
>From: "Jerome Henin" <jhenin_at_cmm.chem.upenn.edu>
>Subject: Re: New ABF order parameters
>To: "Subramanian Vaitheeswaran" <vaithee_at_umd.edu>
>Cc: namdlist <namd-l_at_ks.uiuc.edu>, abf_at_edam.uhp-nancy.fr
>
>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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