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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 10 2010 - 09:30:03 PST
