Re: [AMBER] /dat/slko DFTB files

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Mon, 18 Jul 2011 00:48:20 -0300

Your files are located at:
> /usr/local/amber10/dat/slko

While sander is looking for the files in:
> $(AMBERHOME)/dat/slko/

Then you get the message:
> Missing file:
> /dat/slko/C-C.skf

That means that the $AMBERHOME variable is either not defined correctly, or not being exported to the work nodes in your machine. Notice that it should be defined, in your case, as '/usr/local/amber10'. If you are using bash, the command:

export AMBERHOME=/usr/local/amber10

should solve it.

Good luck,
Gustavo.

--
Sent from my iPad.
On 17/07/2011, at 19:38, Somaye Badieyan <badieyan.gmail.com> wrote:
> Dear Amber users,
> 
> I have received the DFTB parameters required for QM-MM simulation using this
> level of theory. But when I checked the *slko* directory
> (/usr/local/amber10/dat/slko), I found all that parameter files (C-C.skf,
> C-O.skf, ...) are available there. I even check the content of files with
> that ones I have received form DFTB.org and found that they are exactly the
> same. So my question is, do I need to overwite the that files? or am I wrong
> with the directory? I tried to run a minimization job using
> qm_theory='DFTB', but the job stopped, since sander has not found the right
> files (here it mentioned C-C.skf) in /dat/slko directory.
> 
>  Missing file:
>  /dat/slko/C-C.skf
> 
>  Sander could not find the file containing the
>  Slater-Koster integral tables needed. This means
>  either that the file was placed in the wrong
>  directory, is using a different naming scheme,
>  or that you just don't have it.
> 
>  These files are supposd to be located in the
>  $(AMBERHOME)/dat/slko/
>  directory, and be named as <Atom1>-<Atom2>.skf,
>  where <Atom1> and <Atom2> are the atomic symbols.
> 
>  Note that the integral table files needed for
>  a DFTB calculation are not distributed with Amber.
>  To obtain those files, you must point your browser to
>  http://www.dftb.org and follow the instructions
>  to obtain the parameter files.
> 
>  Also, you must make sure that the parameters for the
>  atoms you are interested in exist. Due to the continuous
>  development of new parameters, SANDER NO LONGER DOES
>  THIS CHECK. Rather, Sander only checks for the
>  presence of the parameter file.
> 
> SANDER BOMB in subroutine qm2_dftb_check_slko_file <qm2_dftb_load_params.f>
> File not found.
> Exiting.
> 
> 
> Thanks
> Somaye
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Received on Sun Jul 17 2011 - 21:00:02 PDT