Re: ABF : dihedral-com.tcl

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Nov 21 2007 - 10:36:31 CST

Dear Vaithee,

You need to edit the abf.tcl startup script in order to add the abf0 and
abf3 keywords.

Either you add "abf0 {}" and "abf3 {}" in "array set defaults"
(the same way abf2 is defined there)

Or you add them in "set silent ....." (just add "abf0" and "abf3" after
"direction")

Cheers
vlad

Subramanian Vaitheeswaran wrote:

>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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Dr. Vlad Cojocaru
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e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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