[Dock-fans] amberize_receptor problem

[Scott Brozell]

Hi,

See
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-October/001257.html
and note that the searching problem was fixed
and that the next release of DOCK will have ions and cofactors
libraries for Amber score.

Scott


On Thu, 24 Jan 2008, Osmany Guirola wrote:

> Hi 
> 
> i am runing dock in linux
> and in  the receptor file the line is
> 
> HETATM  334 CA    CA A 201       5.268  20.343   5.202  1.00 11.19          CA
> 
> all CA are uppercase
> 
> 
> 
> 
> ----- Original Message ----
> From: Alessandro Nascimento <al.s.nascimento at gmail.com>
> To: Osmany Guirola <osmany_guirola at yahoo.com>
> Cc: dock-fans at docking.org
> Sent: Thursday, January 24, 2008 11:29:11 AM
> Subject: Re: [Dock-fans] amberize_receptor problem
> 
> 
> Are you running dock in linux? cygwin?
> 
> Can it be caused by case sensitivity ? CA != Ca ??
> 
> HTH,
> 
> 
> --alessandro
> 
> On Jan 24, 2008 11:25 AM, Osmany Guirola <
> osmany_guirola at yahoo.com> wrote:
> 
> Hi 
> I am having problems trying to run the amberize_receptor script 
> my PDB receptor has a Calcium ion  and the script gave me this error
> 
> ......
> .....
> Building topology.
> Building atom parameters.
> 
> For atom: .R<CA 45>.A<CA 1> Could not find type: Ca
> Parameter file was not saved.
>         Quit
> 
> i check the log file  and the script loads the ions library
> Loading library: /home/osmany/progs/dock6/parameters/leap/lib/ions94.lib
> 
> Loading: CA
> Loading: CIO
> Loading: Cl-
> Loading: Cs+
> Loading: IB
> Loading: K+
> Loading: Li+
> Loading: MG
> Loading: MG2
> Loading: Na+
> Loading: Rb+
> Loading: ZN
> 
> What can i do?