From chemistry-request@server.ccl.net Thu May 31 00:37:17 2001
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Date: Thu, 31 May 2001 14:37:11 +1000 (EST)
From: Dave Wilson <chdjw@alinga.newcastle.edu.au>
Subject: g98 compilation error
In-reply-to: <F99TROLINPSusJmdhQN00013f30@hotmail.com>
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I'm trying to compile g98 revision a7 on a dec alpha running tru64 unix
OS. The following error is noted:

/usr/lib/libUfor.a(for_u_getcwd.o): getcwd_: multiply defined
/usr/lib/libUfor.a(etime_.o): etime_: multiply defined
/usr/lib/libUfor.a(loc_.o): loc_: multiply defined
/usr/lib/libUfor.a(time_.o): time_: multiply defined
/usr/lib/libUfor.a(hostnm_.o): hostnm_: multiply defined
Warning: Unresolved:
MAIN__
fort: Severe: Failed while trying to link.

It appears to be a library error, but I have merely copied the libraries
> from another dec alpha with identical OS.

Any help gratefully accepted.

cheers
dave
___________________________________________________________
David Wilson		        University of Newcastle, AUS

chdjw@alinga.newcastle.edu.au
http://quantum.newcastle.edu.au/david


From chemistry-request@server.ccl.net Thu May 31 02:31:47 2001
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Date: Thu, 31 May 2001 22:31:28 +0800 (CST)
From: Fenglou Mao <mao@linux2.ipc.pku.edu.cn>
To: "CHEMISTRY@www.ccl.net" <CHEMISTRY@server.ccl.net>
Subject: non-homology dataset
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Hi, all,
    One or two month ago, someone asked where was
the non-homology dataset, but now I can not find it
in ccl archive, who can tell me where it is? Thx a lot.

-- 
Sincerely Yours,

FengLou Mao
*******************************
ADD:Mr. FengLou Mao
    Institute of Physical Chemistry
    Peking University
    BeiJing
    P.R.China
Tel:86-10-62756833
Fax:86-10-62751725
E-mail:mao@mdl.ipc.pku.edu.cn
Homepage:http://mdl.ipc.pku.edu.cn/~mao


From chemistry-request@server.ccl.net Thu May 31 03:10:44 2001
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Date: Thu, 31 May 2001 09:08:54 +0200 (CEST)
From: David van der Spoel <spoel@xray.bmc.uu.se>
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To: Sergio Manzetti <s.manzetti@student.qut.edu.au>
cc: <chemistry@ccl.net>
Subject: Re: CCL:PDB file structure
In-Reply-To: <991273043.3b15a0533ec3b@email.qut.edu.au>
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On Thu, 31 May 2001, Sergio Manzetti wrote:

>Hi everyone. I have recently understood that many Protein programs don't
>understand a PDB file with only the ATOM and CONECT records. I am attempting to
>dock ligands to a modelled molecule that unfurtunately is not accepted by the
>software (AUTODOCK). Do you have knowledge to which other records are relevant
>for such procedures?
You should be a bit more specific. What exactly does Autodock not like?
Many program neglect the conect records, since they are usually absent
anyway most programs have a database. Anyway, with autodock you do get the
source code, so it should be quite easy to see where the problem is.
Alternatively you grab a pdb file from the pdb databank, compare it to
your own and modify your own accordingly.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel		Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: spoel@xray.bmc.uu.se	www: http://zorn.bmc.uu.se/~spoel
phone:	46 18 471 4205		fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From chemistry-request@server.ccl.net Thu May 31 03:12:03 2001
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Date: Thu, 31 May 2001 17:08:34 +1000
From: Renate Griffith <renateg@mail.newcastle.edu.au>
Subject: CD writer with SG O2 workstation?
To: CHEMISTRY@ccl.net
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Dear all,

has anybody got any experience with writing CDs directly from a Silicon
Graphics O2 workstation? Can I get the necessary hardware and software somewhere?

Regards
Renate

-- 
Dr. Renate Griffith, Lecturer, Discipline of Biological Sciences
School of Biological and Chemical Sciences
Institute of Life Sciences, Life Sciences Building, LS 46
The University of Newcastle
Callaghan, NSW  2308, Australia
Email: renateg@mail.newcastle.edu.au
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From chemistry-request@server.ccl.net Thu May 31 04:36:31 2001
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Date: Thu, 31 May 2001 18:24:41 +1000 (EST)
From: Sergio Manzetti <s.manzetti@student.qut.edu.au>
Subject: AUTODOCK
To: chemistry@ccl.net
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Hi all. I have checked whether my copy of AUTDOCK works or not, testing using
the EXAMPLE files downloadable from the official website.
Again, I got the same error message in the final *dlg file:


(Under  the atomic map files, C, N, O, S, H .map)

autodock3: Filename mismatch:
		"macro.gpf" :: "lig.macro.gpf"


This occurs on ALL my dockings. And it yields the same thing:

A small file (300k) where the ligand packed with itself, out of the reach of the 
macromolecule, not even close to annealed.


Have anyone seen this error message before?

Sergio



Sergio Manzetti
Research Scholar
Centre of Molecular Biotechnology/ Supercomputer Facility
Queensland University of Technology
2 George St.
BRISBANE
4000 QLD
AUSTRALIA
email: s.manzetti@student.qut.edu.au
Tlf: +61 7 3864 1434
Tlf2:+61 7 3864 1185
www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html
www2: http://www.its.qut.edu.au/hpc/

From chemistry-request@server.ccl.net Thu May 31 05:22:40 2001
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Date: Fri, 1 Jun 2001 01:22:16 +0800 (CST)
From: Fenglou Mao <mao@linux2.ipc.pku.edu.cn>
To: "CHEMISTRY@www.ccl.net" <CHEMISTRY@server.ccl.net>
Subject: non-homology subset of PDB
Message-ID: <Pine.LNX.4.21.0106010121290.3704-100000@mdl.ipc.pku.edu.cn>
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Hi, all,
     One or two month ago, someone asked where was
the non-homology subset of PDB, but now I can not find it
in ccl archive, who can tell me where it is? Thx a lot.


-- 
Sincerely Yours,

FengLou Mao
*******************************
ADD:Mr. FengLou Mao
    Institute of Physical Chemistry
    Peking University
    BeiJing
    P.R.China
Tel:86-10-62756833
Fax:86-10-62751725
E-mail:mao@mdl.ipc.pku.edu.cn
Homepage:http://mdl.ipc.pku.edu.cn/~mao


From chemistry-request@server.ccl.net Thu May 31 05:29:24 2001
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From: Hetenyi Csaba <csaba@ovrisc.mdche.u-szeged.hu>
To: David van der Spoel <spoel@xray.bmc.uu.se>
cc: Sergio Manzetti <s.manzetti@student.qut.edu.au>, chemistry@ccl.net
Subject: Re: CCL:PDB file structure
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> On Thu, 31 May 2001, Sergio Manzetti wrote:
> 
> >Hi everyone. I have recently understood that many Protein programs don't
> >understand a PDB file with only the ATOM and CONECT records. I am attempting to
> >dock ligands to a modelled molecule that unfurtunately is not accepted by the
> >software (AUTODOCK). Do you have knowledge to which other records are relevant
> >for such procedures?

Hi,
AutoDock does not need the CONNECT records of the target, only 
ATOM/HETATM records.
Csaba

From chemistry-request@server.ccl.net Thu May 31 06:41:37 2001
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Dear CCL Contributors,

Are there any semi-empiricists familiar with Zindo (or any other) 
who have performed singles and doubles CI for spectroscopic  
purposes. I am having conceptual difficulties deciding how much 
orbital space to include to obtain reasonable ground state 
depressions and corresponding transition energies. It seems that 
the CI space where doubles are generated have to be limited to 
important orbitals or else increasingly lower depressions are 
calculated as the CI space is enlarged. How can one choose 
orbitals selectively without running into the size consistancy 
problem.

Thanks, Scott Kuehl

From chemistry-request@server.ccl.net Thu May 31 07:46:17 2001
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From: "Artem R. Oganov" <a.oganov@ucl.ac.uk>
To: chemistry <chemistry@ccl.net>
Cc: chemistry-request <chemistry-request@ccl.net>
Subject: CCL: Electron density plots
Date: Thu, 31 May 2001 12:44:09 +0100
Message-ID: <NEBBJJFNGLCHAFJKLNJAAEECCEAA.a.oganov@ucl.ac.uk>
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Dear CCLers,

I need a free program for plotting electron density from a file (simple
x,y,z format). Do you have any suggestions? I'd prefer if it works for
Windows; UNIX is also OK. I'll summarise on request.

Cheers,

Artem
-----------------------------------------------------
Artem R. Oganov
Department of Geological Sciences
University College London
Gower Street
London WC1E 6BT

tel: +44 (020)-7679-3344
fax: +44 (020)-7387-1612
email: a.oganov@ucl.ac.uk
http://slamdunk.geol.ucl.ac.uk/~artem
---------------------------------------------------


From chemistry-request@server.ccl.net Thu May 31 09:03:03 2001
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Date: Thu, 31 May 2001 15:02:05 +0200
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Subject: Re: CCL:Electron density plots
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I think what you need is Molden:

http://www.cmbi.kun.nl/~schaft/molden/molden.html

best regards
modest

"Artem R. Oganov" wrote:

> Dear CCLers,
>
> I need a free program for plotting electron density from a file (simple
> x,y,z format). Do you have any suggestions? I'd prefer if it works for
> Windows; UNIX is also OK. I'll summarise on request.
>
> Cheers,
>
> Artem
> -----------------------------------------------------
> Artem R. Oganov
> Department of Geological Sciences
> University College London
> Gower Street
> London WC1E 6BT
>
> tel: +44 (020)-7679-3344
> fax: +44 (020)-7387-1612
> email: a.oganov@ucl.ac.uk
> http://slamdunk.geol.ucl.ac.uk/~artem
> ---------------------------------------------------
>
> -= This is automatically added to each message by mailing script =-
> CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
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--
modest@pharmazie.uni-wuerzburg.de

Modest von Korff
Institut fuer Pharmazie
Am Hubland
Universitaet Wuerzburg
97073 Wuerzburg
Germany

#0931 888 5473



From chemistry-request@server.ccl.net Thu May 31 15:55:10 2001
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Date: Thu, 31 May 2001 21:55:07 +0200 (METDST)
From: Frank Jensen <frj@dou.dk>
To: chemistry@ccl.net
Subject: DFT - Spherical atoms
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	Dear all,
	
	I am looking for software capable of performing
DFT calculations on atoms using average-of-states wave
functions and standard Gaussian basis functions for expanding
the orbitals.

	An example: the F-atom has the occupancy
1s2 2s2 2px2 2py2 2pz1. A standard ROHF calculation
will break the full spherical symmetry, producing
two different orbital energies for the p-orbitals
(px = py != pz). The full symmetry corresponds to 
an occupancy of 1s2 2s2 2px(5/3) 2py(5/3) 2pz(5/3). 
Such a wave function can be generated by programs capable
of GVB calculations, or more general, programs
which can do average-of-states wave functions.

	Now the question: does anyone know of a program 
which can do such average-of-state wave function with 
a DFT functional, instead of HF, and using a Gaussian
basis set for expanding the orbitals?

	Frank

	

--------------------------------------------------
| Frank Jensen, Department of Chemistry          |
| SDU Odense University, DK-5230 Odense, Denmark |
| FAX +45 66 15 87 80 , Voice +45 65 50 25 07    |
| http://www.sdu.dk/Nat/Chem/STAFF/sci/FrjE.html |
| http://bogense.chem.ou.dk/~frj                 |
--------------------------------------------------


From chemistry-request@server.ccl.net Thu May 31 17:42:34 2001
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Hola, estoy corriendo en Gaussian una optimizacion de geometria y tengo
exito cuando 
no uso simetria (NoSymm) pero cuando dejo el default que es usar simetria no
tengo exito y 
la optimizacion fracasa. Alguna sugerencia?.


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Date: Thu, 31 May 2001 19:14:26 -0300 (ARST)
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To: chemistry@ccl.net
From: Pablo Albores <albores@q1.fcen.uba.ar>
Subject: pregunta

Hello, i am working in a geometry optimization with gaussian
and i only find good results when i disable the simmetry option, instead
with simmetry option
enable the process dies.
Any suggestion? Thanks.


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Date: Fri, 1 Jun 2001 11:06:17 +1000
To: biomol@molsci.csiro.au, chemistry@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU
From: "Dr. Dave Winkler" <Dave.Winkler@molsci.csiro.au>
Subject: Speakers/program for drug design theme of IUPAC World Chemistry
 Congress

The IUPAc World Chemistry Congress is only a month away.  The Congress will
be held in Brisbane, Australia 1-6 July 2001.  The web site is
http://www.ccm.com.au/wcc.  There is a great lineup of international
speakers which can be viewed at the AIMECS web site
http://www.aimecs.org/timetable.html.

I hope to see many of you at this meeting, especially those international
visitors who caught a glimpse of Australia during the Olympics and have
been looking for a reason to visit.

Cheers,

Dave

Dr. David A. Winkler                    Email: dave.winkler@molsci.csiro.au
Senior Principal Research Scientist     Voice: 61-3-9545-2477
CSIRO Molecular Science			Fax:   61-3-9545-2446
Private Bag 10,Clayton South MDC 3169   http://www.csiro.au
Australia 	        		http://www.molsci.csiro.au

For the World Chemical Congress in Brisbane, July 2001 check the details at
http://www.ccm.com.au/wcc




