From chemistry-request@server.ccl.net Fri Jun 28 01:20:13 2002
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Date: Fri, 28 Jun 2002 15:21:27 +1000
Subject: DOCK 4.0 Error Message
From: Michael Ivery <michaeli@pharm.usyd.edu.au>
To: <chemistry@ccl.net>
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Dear All,

I am trying to use DOCK 4.0 for first time. On running dock demo_script get
error message ERROR get-parameters Chemical Screen Intervals >30!

Does anyone know what this means.

Best Wishes

Michael Ivery
Faculty of Pharmacy University of Sydney

e-mail: michaeli@pharm.usyd.edu.au


From chemistry-request@server.ccl.net Fri Jun 28 03:39:59 2002
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Date: Fri, 28 Jun 2002 09:39:53 +0200 (MEST)
From: konietz@uni-duesseldorf.de
Subject: Was: Semiempirical AIM
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Hello,

the problem of semiempirical AIM seems to be the same as for AIM with
ECPs. This was discussed on the list before. Because of the lack of core
density.
I am mixing ECP Basis sets and 6-31g kinds of basis sets. Is it also
dangerous to analyse critical points between atoms with core density when
there is an atom somewhere else in the molecule with no core density? From
my understanding it is not.
Am i missing something?

Thanks in advance,

Stefan.


From chemistry-request@server.ccl.net Fri Jun 28 05:25:25 2002
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From: Szilveszter Juhos <szilva@ribotargets.com>
To: Joe Leonard <jle@theworld.com>
cc: chemistry@ccl.net
Subject: Re: CCL:C Hacker question
In-Reply-To: <5.1.0.14.1.20020627210520.0239a220@pop.theworld.com>
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On Thu, 27 Jun 2002, Joe Leonard wrote:

> Does anybody know a way to determine the name of the calling
> routine from C - Routine A calls Routine B, and B wishes to know
> the name of whatever routine called it...

If you compile with -g (and no optimization) than debug it? cvd under SGI
is a very neat stuff or ddd/gdb under Linux. Even easier check the xref of
the sourece tree (ie in [x]emacs or sourcenavigator) or use ctags. M-x 
speedbar can help a lot in xemacs, ctags-exuberant in vim.

Cheers
Szilva




From chemistry-request@server.ccl.net Fri Jun 28 05:55:29 2002
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Date: Fri, 28 Jun 2002 12:01:40 +0200 (CEST)
From: "Rafael R. Pappalardo" <rafapa@simulux.us.es>
To: Jim Stoner <jstoner@du.edu>
cc: <chemistry@ccl.net>, <help@gaussian.com>
Subject: Re: CCL:G98 A11.1 and SMP under RedHat 2.4
In-Reply-To: <CBEHKOIKBBDKKJDFKBJFEELJCGAA.jstoner@du.edu>
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On Thu, 27 Jun 2002, Jim Stoner wrote:

> Hi all
> Thanks for your time.  I am having a killer of a time getting G98 to build
> with smp support.  I am using the current version of PGI F77.  The box I am
> using is a Dell Precision 530 w/ 1GB of RAM.  The system environment is:
>
> # uname -a
> Linux strontium 2.4.9-21smp #1 SMP Thu Jan 17 14:01:48 EST 2002 i686 unknown
>
> Other applications compile and run under SMP with no problem.  However, G98
> kicks back the following in the logfile before it seg/malloc faults and core
> dumps from:
>
> # g98 ./2proctest.com ./ &
> [2] 1489
> # shmget failed.: Invalid argument
> [2]    Exit 1                        g98 ./2proctest.com ./

Have you changed the value of shmmax? I need to do something like

echo "805306368" >/proc/sys/kernel/shmmax

Where 805306368 is the amount of memory in bytes (768Mb in the example).

I normally include the line in the /etc/rc.d/rc.local file to be sure
is run at every reboot.

Hope this helps.

Rafael

> #
>
> <snip logifile>
> ***********************************************
>  Gaussian 98:  x86-Linux-G98RevA.11.1 1-Nov-2001
>                    27-Jun-2002
>  ***********************************************
>  %Chk=js3-5.chk
>  %mem=50MB
>  %NPROC=2
>  Will use up to    2 processors via shared memory.
>  -------------------------
>  #P UHF/6-31G Opt PROP=epr
>  -------------------------
>  1/18=20,38=1/1,3;
>  2/9=110,17=6,18=5,40=1/2;
>  3/5=1,6=6,11=2,25=1,30=1/1,2,3;
>  4/7=2/1;
>  5/5=2,38=4/2;
>  6/7=2,8=2,9=2,10=2,17=2,26=4,28=1/1,2;
>  7//1,2,3,16;
>  1/18=20/3(1);
>  99//99;
>  2/9=110/2;
>  3/5=1,6=6,11=2,25=1,30=1/1,2,3;
>  4/5=5,7=2,16=2/1;
>  5/5=2,38=4/2;
>  7//1,2,3,16;
>  1/18=20/3(-5);
>  2/9=110/2;
>  6/7=2,8=2,9=2,10=2,17=2,19=2,26=4,28=1/1,2;
>  99/9=1/99;
>  Leave Link    1 at Thu Jun 27 20:22:55 2002, MaxMem=    6553600 cpu:
> 0.1
> <snip logifile>
>
> If I try to specify 2 processors and worse, if I reduce the memory
> allocation even farther so it thinks it has enough, then it starts stating
> it is reducing the number of processors and evoking LINDA.  Any ideas?
>
> Thanks again,
> Jim
>
>
> PS.  Has anyone seen a substantial increases in production by envoking ATLAS
> instead of BLAS?  Is it worth getting A11.3 for the ATLAS build?  All
> thoughts would be gratefully appreciated...
>
>
> =====================================
> James W. Stoner
> Doctoral Student
> University of Denver
> Department of Chemistry and Biochemistry
> Eaton Electron Paramagnetic Resonance Labs
> =====================================
>
>
>
> -= This is automatically added to each message by mailing script =-
> CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net
>
>
>
>
>

-- 
Dr. Rafael R. Pappalardo
Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain)
e-mail: rafapa@simulux.us.es


From chemistry-request@server.ccl.net Fri Jun 28 05:15:06 2002
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To: Joe Leonard <jle@theworld.com>
Cc: chemistry@ccl.net
Subject: Re: C Hacker question
References: <5.1.0.14.1.20020627210520.0239a220@pop.theworld.com>
From: Andrey Khavryuchenko <akhavr@kds.com.ua>
Organization: KDS Software Group
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Joe,

"JL" == Joe Leonard wrote:

 JL> Does anybody know a way to determine the name of the calling
 JL> routine from C - Routine A calls Routine B, and B wishes to know
 JL> the name of whatever routine called it...

 JL> If it's a real hack, something which works on Linux (or Linux and SGI)
 JL> would do the trick. Pointers to these kinds of programmer tricks
 JL> are appreciated as well!

If you're developing such code, you'd better to supply an additional flag,
which signifies who called the B routine.

Otherwise, you have to build debug version of your program (with symbols)
and do hard tricks parsing gdb output.

I wonder why would you need that?

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development


From chemistry-request@server.ccl.net Fri Jun 28 06:28:58 2002
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From: "Victor Anisimov" <victor@fqspl.com.pl>
To: <konietz@uni-duesseldorf.de>, <chemistry@ccl.net>
References: <Pine.SOL.4.21.0206280930010.281-100000@neptun>
Subject: Re: CCL:Was: Semiempirical AIM
Date: Fri, 28 Jun 2002 12:31:03 +0200
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Hi Stefan and all CCLers,

The problem between nonempirical and semiempirical AIM is slightely
in a different phase. There is a very good paper, describing a nature of the
NDDO functional:

P.L.Cummins, S.J.Titmus, D.Jayatilaka, A.A.Bliznyuk, A.P.Rendell, J.E.Grady
Chem.Phys.Letters, 353 (2002) 245-251

With best regards,
Victor.

Victor Anisimov,
FQS Poland, Fujitsu
ul. Starowislna 13-15, 31-038 Krakow, Poland
Email: victor@fqspl.com.pl
Web: http://www.fqspl.com.pl
Tel.(+48 12) 429-4345  Fax(+48 12) 429-6124


----- Original Message -----
From: <konietz@uni-duesseldorf.de>
To: <chemistry@ccl.net>
Sent: Friday, June 28, 2002 9:39 AM
Subject: CCL:Was: Semiempirical AIM


>
> Hello,
>
> the problem of semiempirical AIM seems to be the same as for AIM with
> ECPs. This was discussed on the list before. Because of the lack of core
> density.
> I am mixing ECP Basis sets and 6-31g kinds of basis sets. Is it also
> dangerous to analyse critical points between atoms with core density when
> there is an atom somewhere else in the molecule with no core density? From
> my understanding it is not.
> Am i missing something?
>
> Thanks in advance,
>
> Stefan.




From chemistry-request@server.ccl.net Fri Jun 28 07:27:17 2002
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From: =?iso-8859-1?Q?Jes=FAs_Rodr=EDguez_Otero?= <qftjesus@usc.es>
To: <chemistry@ccl.net>
Subject: problems with IRC (command downhill)
Date: Fri, 28 Jun 2002 13:28:19 +0200
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This is a multi-part message in MIME format.

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Hi netters

I have a problem with the IRC in Gaussian 98
The manual says that the option DOWNHILL follow the reaction path =
downhill from a starting point that is not a transition state. But this =
is not correct, because this option is not accepted by the program:

*************************************************************************=
***************************
 TestRt Revision:  G98A.9
 Please type in the route specification, terminated with a blank line:
#n rhf/6-31g irc=3Ddownhill

 -------------------------
 #n rhf/6-31g irc=3Ddownhill
 -------------------------
  QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.
 #N RHF/6-31G IRC=3DDOWNHILL
                               '
 Last state=3D"IRC1"
 TCursr=3D 9814 LCursr=3D  17
 Error termination via Lnk1e
*************************************************************************=
**************

The option 'downhill' gives a syntax error !!

What happens??

Thanks in advance

Jesus Rodriguez Otero


------=_NextPart_000_0063_01C21EA7.AAC4EF80
Content-Type: text/html;
	charset="iso-8859-1"
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.2600.0" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Hi netters</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I have a problem with the IRC in =
Gaussian=20
98</FONT></DIV>
<DIV><FONT size=3D2><FONT face=3DArial>The manual says that the option =
DOWNHILL=20
follow the reaction path downhill from a starting point that is not a =
transition=20
state. <FONT size=3D3><FONT size=3D2>But this is not correct, because =
this option is=20
not accepted by the program:</FONT></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial=20
size=3D2>****************************************************************=
************************************</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;TestRt Revision:&nbsp; =
G98A.9<BR>&nbsp;Please=20
type in the route specification, terminated with a blank line:<BR>#n =
rhf/6-31g=20
irc=3Ddownhill</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial =
size=3D2>&nbsp;-------------------------<BR>&nbsp;#n=20
rhf/6-31g irc=3Ddownhill<BR>&nbsp;-------------------------<BR>&nbsp; =
QPERR --- A=20
SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.<BR>&nbsp;#N RHF/6-31G=20
IRC=3DDOWNHILL</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;=20
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
'<BR>&nbsp;Last state=3D"IRC1"<BR>&nbsp;TCursr=3D 9814 LCursr=3D&nbsp;=20
17<BR>&nbsp;Error termination via Lnk1e</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>****************************************************************=
***********************</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>The option 'downhill' gives a syntax =
error=20
!!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>What happens??</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thanks in advance</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Jesus Rodriguez Otero</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV></BODY></HTML>

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From chemistry-request@server.ccl.net Fri Jun 28 08:33:30 2002
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Date: Fri, 28 Jun 2002 08:33:29 -0400 (EDT)
From: "Cherif F. Matta" <cmatta@chem.utoronto.ca>
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To: CHEMISTRY@ccl.net
Subject: Geometry Optimization of a large Silicon cluster
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Dear CCLers,

I would very much appreciate any tip from you about the following
question:

I am trying to optimize quite a large silicon cluster (67 Si atoms + 
46 H atoms) representing the Si(111) 7x7 reconstructed surface.  

I have a lot of problems optimizing it even using the modest RHF/3-21G.  
What would be the best ECP that I can use to speed up this calculation 
and bring it to the realm of possibility? Are the geometies 
optimized using ECPs known to be good and reproduce experimental 
geometries?

Any other suggestions would be highly appreciated.

Thank you very much.  (I will summarize).

    Cherif
    
  ----------------------------------
  Chérif F. Matta,
  Theoretical/Computational Chemist,
  Polanyi Research Group,
  Lash Miller Chemical Laboratories,
  Chemistry Department,
  University of Toronto,
  80 St. George Street (Room 261),
  Toronto, Ontario, Canada M5S 1A1.
  ...................................
  Telephone:      (416) 978 - 3625
  Cellular:       (416) 996 - 2444
  Fax:            (416) 978 - 7580
  http://chem.utoronto.ca/~cmatta/
  -----------------------------------





From chemistry-request@server.ccl.net Fri Jun 28 12:34:20 2002
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CC: Joe Leonard <jle@theworld.com>
Subject: Re: CCL:C Hacker question
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Andrey Khavryuchenko wrote:
> Joe,
> 
> "JL" == Joe Leonard wrote:
> 
>  JL> Does anybody know a way to determine the name of the calling
>  JL> routine from C - Routine A calls Routine B, and B wishes to know
>  JL> the name of whatever routine called it...
> 
>  JL> If it's a real hack, something which works on Linux (or Linux and SGI)
>  JL> would do the trick. Pointers to these kinds of programmer tricks
>  JL> are appreciated as well!
> 
> If you're developing such code, you'd better to supply an additional flag,
> which signifies who called the B routine.
> 
> Otherwise, you have to build debug version of your program (with symbols)
> and do hard tricks parsing gdb output.


Actually, it could be solved by compiling with symbols, and then doing 
stack unwinding to find the function pointer of the calling function and 
then looking that up in the symbol table.

It could by done, but it's not really appropriate for this list (Usenet 
has groups full of people who can answer this) nor is it an advisable 
technique.

Dave



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From: "dakshanamurthy sivanesan" <siva@is.aist-nara.ac.jp>
To: <chemistry@ccl.net>
Subject: Grasp-Question
Date: Fri, 28 Jun 2002 23:09:15 +0900
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Dear CCLers:

I have some questions:

First of all I describe Aim of my ElectroStatic Potential surface =
calculation using GRASP:

1. I want to generate ESP surface around each protein in the PDB without =
a ligand (i.e. HET. atoms) inside the binding site.
2. Then keep (show) the ligands (several)  in the active site and look =
for the ESP surface patterns to see any new signatures.
3. How can I show the ligands inside the active site in presence of ESP =
surface=20

at this point I have questions:

1. First of all Whether Do I need to include hydrogens in the PDB =
structure.
2. If I don,t what should be done for assigning charges.
3. Or If I want to use hydrogens then what should I do for charges.

Thanks in advance,

Sincerely,
D.Sivanesan

D. Sivanesan, Ph.D.,
Post doctoral Associate Fellow,
Graduate School of Information Science,
Nara Institute of Science & Technology,
8916-5, Takayama,
Ikoma, Nara 630-01 JAPAN
E-mail: siva@is.aist-nara.ac.jp
Tel: 0743-72-5611

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<BODY bgColor=3D#ffffff>
<DIV>
<DIV>Dear CCLers:<BR><BR>I have some questions:<BR><BR>First of all I =
describe=20
Aim of my ElectroStatic Potential surface calculation using =
GRASP:<BR><BR>1. I=20
want to generate ESP surface around each protein in the PDB without a =
ligand=20
(i.e. HET. atoms) inside the binding site.<BR>2. Then keep (show) the =
ligands=20
(several)&nbsp; in the active site and look for the ESP surface patterns =
to see=20
any new signatures.<BR>3. How can I show the ligands inside the active =
site in=20
presence of ESP surface <BR><BR>at this point I have =
questions:<BR><BR>1. First=20
of all Whether Do I need to include hydrogens in the PDB =
structure.<BR>2. If I=20
don,t what should be done for assigning charges.<BR>3. Or If I want to =
use=20
hydrogens then what should I do for charges.<BR><BR>Thanks in=20
advance,<BR><BR>Sincerely,<BR>D.Sivanesan<BR></DIV></DIV>
<DIV>D. Sivanesan, Ph.D.,<BR>Post doctoral Associate Fellow,<BR>Graduate =
School=20
of Information Science,<BR>Nara Institute of Science &amp;=20
Technology,<BR>8916-5, Takayama,<BR>Ikoma, Nara 630-01 JAPAN<BR>E-mail: =
<A=20
href=3D"mailto:siva@is.aist-nara.ac.jp">siva@is.aist-nara.ac.jp</A><BR>Te=
l:=20
0743-72-5611</DIV></BODY></HTML>

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From chemistry-request@server.ccl.net Fri Jun 28 16:34:10 2002
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Date: Fri, 28 Jun 2002 16:34:08 -0400 (EDT)
From: avijit ghosh <avijit@CS.Cornell.EDU>
To: chemistry@ccl.net
Subject: Re: C Hacker Question
Message-ID: <Pine.LNX.4.44.0206281615000.21836-100000@fafe.cs.cornell.edu>
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>Folks,

>Does anybody know a way to determine the name of the calling
>routine from C - Routine A calls Routine B, and B wishes to know
>the name of whatever routine called it...

>If it's a real hack, something which works on Linux (or Linux and SGI)
>would do the trick. Pointers to these kinds of programmer tricks
>are appreciated as well!

	This is a bit off the top of my head but what I would do is write 
a simple perl script (or perhaps you could just do it w/ defines) that 
appends to all your C calls __FUNCTION__ as the last argument. This is a 
gnu extension that tells you the name of the current routine. The same 
perl script would also append to each function declaration a   char 
*whoCalledMe). To make things easy use a define that does nothing for your 
perl script to snag the subroutines you want appended in this manner .

i.e

	DEBUGME(myfunction)(double x,double y, double z);

(so parse twice once for subroutine names and then for calls). Of course 
now your  code is dependent on a perl script (never good!) but hopefully 
this is for  debugging so you it'll only be embarrassing for yourself :)
You could probably make a few defines so as to leave the code in but 
compiled out at will as well as  for printing the caller subroutine name 
trivially.

There is probably an equivalent trick for fortran (or any other  language) 
that could be worked out.

	Best regards,
	-avi


