AMBER Archive (2007)

Subject: AMBER: RE: RE: AMBER: Problem with SCC-DFTB parameter files

From: ÇÑÀç¹ü (hanjb77_at_naver.com)
Date: Fri May 04 2007 - 23:25:29 CDT

Thanky you, all!
I could simulate my system after changing the owner of AMBER9 directory from root to me.
It might be the permission problem.
Thank you.

Jaebeom

-----Original Message-----
From: "Ross Walker"<ross_at_rosswalker.co.uk>
To: amber_at_scripps.edu
Cc:
Sent: 07-05-02(¼ö) 23:45:07
Subject: RE: AMBER: Problem with SCC-DFTB parameter files

Hi Jaebeom,

Just to check does the following file actually exist? /usr/local/amber9-
serial/dat/slko/nn.spl

If not then what is the contents of the /usr/local/amber9-serial/dat/slko/
directory?

Also check that the username under which sander is running has permission
to see this directory. And if you are running this on a cluster make sure
the node on which the job runs can also see the same directory and files.

Good luck....
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of ???
> Sent: Tuesday, May 01, 2007 21:55
> To: amber_at_scripps.edu
> Subject: AMBER: Problem with SCC-DFTB parameter files
>
> 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_at_phys.uni-paderborn.de
> Fax: +49-(0)5251-60-3435
>
>
> SANDER BOMB in subroutine qm2_dftb_check_slko_file
> <qm2_dftb_load_params.f>
> 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
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

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