Re: [AMBER] about dihedralcluster

From: Balazs Jojart <jojartb.gmail.com>
Date: Wed, 10 Nov 2010 20:36:52 +0100

Dear Dan,
Thank you very much for the answer!
Balazs

On 11/10/2010 06:04 PM, Daniel Roe wrote:
> Unfortunately there is a typo in the AmberTools user manual - the
> actual command is 'clusterdihedral', not 'dihedralcluster', sorry.
>
> The format of the dihedralfile should be for each dihedral
>
> ATOM#1 ATOM#2 ATOM#3 ATOM#4 bins
>
> Where ATOM#1-4 are integers representing the actual atom numbers (not
> masks) of the atoms involved in the dihedral, and bins is an integer
> representing the desired number of bins. So something like:
>
> 5 7 9 15 10
> 7 9 15 17 10
>
> would be valid.
>
> -Dan
>
>
> On Wed, Nov 10, 2010 at 7:56 AM, Balazs Jojart<jojartb.gmail.com> wrote:
>> Dear Users,
>> I tried to perform dihedralcluster analysis for the sidechain dihedrals
>> which belongs to the active site of a receptor.
>> Unfortunately I obtain always the following error message:
>>
>>
>> ERROR in tokenize(): wrong syntax
>> PTRAJ: dihedralcluster out test.OUT framefile test.FRAMEFILE clusterinfo
>> test.CLUSTERINFO dihedralfile dihedralcluster
>>
>> The following syntaxes were used in the dihedralcluster file:
>>
>> :66.N :66.CA :66.CB :66.CG1 10
>>
>> 988 990 992 998 10
>>
>> .988 @990 @992 @998 10
>>
>> Which format should be used in the dihedralfile?
>>
>> Thank you very much for your help in advance!
>> Balazs Jojart
>>
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>>
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-- 
Balazs Jojart, Ph.D.
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Received on Wed Nov 10 2010 - 12:00:03 PST
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