Re: AMBER: Problem with SCC-DFTB parameter files

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Wed, 02 May 2007 07:46:58 -0400

Hi Jaebeom,

This message is generated when sander can't find the DFTB parameters in
the correct place. Where exactly did you place the files? According to
the output, they must be in

/usr/local/amber9-serial/dat/slko/


Which is inside *your* (redefined) AMBERHOME. Can you access these files
there?

Also, are you running it locally or in a remote computer/cluster? Is
there any chance that the computer you are running cannot access this
directory, or does not have read access to it?

Gustavo.


wrote:
> Hello, users.
>
> I want to use SCC-DFTB for QM/MM simulation, and I put the parameter files in $AMBERHOME/dat/slko directory.
> However, when I started my simulation, I encountered the error message as follows:
>
> --------------------------------------------------------------------------------
> 3.1 QM CALCULATION INFO
> --------------------------------------------------------------------------------
>
> QMMM: SINGLET STATE CALCULATION
> QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 8
> DFTB: Number of atom types = 3
>
> Parameter files:
> TYP (AT) TYP (AT) SK integral FILE
> | 1 1 (n ) 1 (n ) /usr/local/amber9-serial/dat/slko/nn.spl
> ****************************************************
> * !! A FILE NEEDED BY DFTB WAS NOT FOUND !! *
> ****************************************************
>
> 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, or that you don't have it.
>
> These files are supposd to be located in the
> $(AMBERHOME)/dat/slko/
> directory.
>
> Notice that the integral table files needed for
> a DFTB calculation are not distributed with Amber.
> To obtain those files, you must fill and sign the
> license agreement found on the file:
>
> $(AMBERHOME)/doc/DFTB_license.pdf
>
> and fax/mail/e-mail it directly to:
>
> JunProf. Dr. Marcus Elstner
> Theoretical Physics
> University of Paderborn
> Pohlweg 55, Building N,
> 33098 Paderborn
> Germany
>
> E-Mail: elstner.phys.uni-paderborn.de
> Fax: +49-(0)5251-60-3435
>
>
> SANDER BOMB in subroutine qm2_dftb_check_slko_file &lt;qm2_dftb_load_params.f&gt;
> File not found.
> Exiting.
>
>
> The spl files are those sent by Dr. Elstner when my lab requested him for SCC-DFTB/MM simulation with CHARMM about two years ago, so I don't think that the spl files have problems. The computer that I used has also amber8, so I changed the directory of AMBERHOME into /usr/local/amber9-serial/ only for me. I want to know what to change and how to change the configuration of the computer.
>
> Thank you
> Jaebeom
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Received on Sun May 06 2007 - 06:07:05 PDT
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