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

From: 한재범 <hanjb77.naver.com>
Date: Sat, 05 May 2007 13:25:29 +0900

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: &quot;Ross Walker&quot;&lt;ross.rosswalker.co.uk&gt;
To: amber.scripps.edu
Cc:
Sent: 07-05-02(수) 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

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| San Diego Supercomputer Center |
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&gt; -----Original Message-----
&gt; From: owner-amber.scripps.edu
&gt; [mailto:owner-amber.scripps.edu] On Behalf Of ???
&gt; Sent: Tuesday, May 01, 2007 21:55
&gt; To: amber.scripps.edu
&gt; Subject: AMBER: Problem with SCC-DFTB parameter files
&gt;
&gt; Hello, users.
&gt;
&gt; I want to use SCC-DFTB for QM/MM simulation, and I put the
&gt; parameter files in $AMBERHOME/dat/slko directory.
&gt; However, when I started my simulation, I encountered the
&gt; error message as follows:
&gt;
&gt; --------------------------------------------------------------
&gt; ------------------
&gt; 3.1 QM CALCULATION INFO
&gt; --------------------------------------------------------------
&gt; ------------------
&gt;
&gt; QMMM: SINGLET STATE CALCULATION
&gt; QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 8
&gt; DFTB: Number of atom types = 3
&gt;
&gt; Parameter files:
&gt; TYP (AT) TYP (AT) SK integral FILE
&gt; | 1 1 (n ) 1 (n ) /usr/local/amber9-serial/dat/slko/nn.spl
&gt; ****************************************************
&gt; * !! A FILE NEEDED BY DFTB WAS NOT FOUND !! *
&gt; ****************************************************
&gt;
&gt; Sander could not find the file containing the
&gt; Slater-Koster integral tables needed. This means
&gt; either that the file was placed in the wrong
&gt; directory, or that you don't have it.
&gt;
&gt; These files are supposd to be located in the
&gt; $(AMBERHOME)/dat/slko/
&gt; directory.
&gt;
&gt; Notice that the integral table files needed for
&gt; a DFTB calculation are not distributed with Amber.
&gt; To obtain those files, you must fill and sign the
&gt; license agreement found on the file:
&gt;
&gt; $(AMBERHOME)/doc/DFTB_license.pdf
&gt;
&gt; and fax/mail/e-mail it directly to:
&gt;
&gt; JunProf. Dr. Marcus Elstner
&gt; Theoretical Physics
&gt; University of Paderborn
&gt; Pohlweg 55, Building N,
&gt; 33098 Paderborn
&gt; Germany
&gt;
&gt; E-Mail: elstner.phys.uni-paderborn.de
&gt; Fax: +49-(0)5251-60-3435
&gt;
&gt;
&gt; SANDER BOMB in subroutine qm2_dftb_check_slko_file
&gt; &lt;qm2_dftb_load_params.f&gt;
&gt; File not found.
&gt; Exiting.
&gt;
&gt;
&gt; The spl files are those sent by Dr. Elstner when my lab
&gt; requested him for SCC-DFTB/MM simulation with CHARMM about
&gt; two years ago, so I don't think that the spl files have
&gt; problems. The computer that I used has also amber8, so I
&gt; changed the directory of AMBERHOME into
&gt; /usr/local/amber9-serial/ only for me. I want to know what to
&gt; change and how to change the configuration of the computer.
&gt;
&gt; Thank you
&gt; Jaebeom
&gt; --------------------------------------------------------------
&gt; ---------
&gt; The AMBER Mail Reflector
&gt; To post, send mail to amber.scripps.edu
&gt; To unsubscribe, send &quot;unsubscribe amber&quot; to majordomo.scripps.edu
&gt;


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Received on Sun May 06 2007 - 06:07:35 PDT
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