From owner-chemistry@ccl.net Fri Dec  1 01:32:00 2006
From: "Joaquin Barroso Flores joaco_barroso~!~yahoo.com" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL:G: ONIOM error -- GetSCM: Allocation for LST2 failed:
Message-Id: <-33136-061130003206-16883-iw4K6o9Fx6wW5usy2sP+zA{:}server.ccl.net>
X-Original-From: Joaquin Barroso Flores <joaco_barroso!^!yahoo.com>
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Date: Wed, 29 Nov 2006 22:31:57 -0600 (CST)
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Sent to CCL by: Joaquin Barroso Flores [joaco_barroso^^yahoo.com]

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Hi Alan
   
  Check out the line of the error regarding how much disk space you need and how much you have available. You have to change the g03 settings to allow it to use more disk space
   
  cheers
   
  Joaquin
>>>>Core=-1707151352 Need=1090405693 GauSpace=-1707151352 MaxMem=52428800
Avail=52428800.<<<<<

  "Gibbs, Alan C. PRDUS AGIBBS%prdus.jnj.com" <owner-chemistry^ccl.net> escribió:
  Sent to CCL by: "Gibbs, Alan C. [PRDUS]" [AGIBBS^-^prdus.jnj.com]
This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

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Hi CCLers,
I'm having trouble with a G03 ONIOM job which dies after the following
message:

..
ONIOM: calculating electric field derivatives.
ONIOM: Dipole =-2.32696873D+00 4.33938853D+00 2.73808494D+00
ONIOM: Dipole moment (Debye):
X= -5.9146 Y= 11.0296 Z= 6.9595 Tot= 14.3202
ONIOM: Integrating ONIOM file 5 number 695
GetSCM: Allocation for LST2 failed:
Core=-1707151352 Need=1090405693 GauSpace=-1707151352 MaxMem=52428800
Avail=52428800.
Error termination via Lnk1e in /local//g03/l107.exe at Wed Nov 29 00:07:52
2006.
Job cpu time: 0 days 13 hours 50 minutes 26.6 seconds.
File lengths (MBytes): RWF= 468 Int= 0 D2E= 0 Chk= 167
Scr= 1

[route card= # opt oniom(b3lyp/6-311++g(2d,p):am1:uff) geom=connectivity
scf=xqc opt=loose ]

Has anyone else experienced this error?
Any insight as to what is wrong is much appreciated.
Al

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  charset=3Diso-8859-1">
  5.5.2658.34">




  Hi CCLers,

I'm having trouble with a G03 ONIOM job which dies =
after the following message:



  ...

 ONIOM: calculating electric field =
derivatives.

 ONIOM: =
Dipole        =3D-2.32696873D+00 =
4.33938853D+00 2.73808494D+00

 ONIOM: Dipole moment (Debye):

    X=3D    =
-5.9146    Y=3D    =
11.0296    Z=3D     6.9595  =
Tot=3D    14.3202

 ONIOM: Integrating ONIOM file  5 =
number   695

GetSCM:  Allocation for LST2   =
failed:

Core=3D-1707151352 Need=3D1090405693 =
GauSpace=3D-1707151352 MaxMem=3D52428800 Avail=3D52428800.

 Error termination via Lnk1e in =
/local//g03/l107.exe at Wed Nov 29 00:07:52 2006.

 Job cpu time:  0 days 13 hours 50 minutes =
26.6 seconds.

 File lengths (MBytes):  =
RWF=3D    468 Int=3D      0 =
D2E=3D      0 Chk=3D    167 =
Scr=3D      1



  [route card=3D # opt =
oniom(b3lyp/6-311++g(2d,p):am1:uff) geom=3Dconnectivity scf=3Dxqc =
opt=3Dloose ]



  Has anyone else experienced this error?

Any insight as to what is wrong is much =
appreciated.

Al





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<div>Hi Alan</div>  <div>&nbsp;</div>  <div>Check out the line of the error regarding how much disk space you need and how much you have available. You have to change the g03 settings to allow it to use more disk space</div>  <div>&nbsp;</div>  <div>cheers</div>  <div>&nbsp;</div>  <div>Joaquin<BR>&gt;&gt;&gt;&gt;Core=-1707151352 Need=1090405693 GauSpace=-1707151352 MaxMem=52428800<BR>Avail=52428800.&lt;&lt;&lt;&lt;&lt;<BR><B><I></I></B></div>  <div><B><I>"Gibbs, Alan C. PRDUS AGIBBS%prdus.jnj.com" &lt;owner-chemistry^ccl.net&gt;</I></B> escribió:</div>  <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Sent to CCL by: "Gibbs, Alan C. [PRDUS]" [AGIBBS^-^prdus.jnj.com]<BR>This message is in MIME format. Since your mail reader does not understand<BR>this format, some or all of this message may not be legible.<BR><BR>------_=_NextPart_001_01C713C5.71DF1BB4<BR>Content-Type: text/plain;<BR>charset="iso-8859-1"<BR><BR>Hi
 CCLers,<BR>I'm having trouble with a G03 ONIOM job which dies after the following<BR>message:<BR><BR>..<BR>ONIOM: calculating electric field derivatives.<BR>ONIOM: Dipole =-2.32696873D+00 4.33938853D+00 2.73808494D+00<BR>ONIOM: Dipole moment (Debye):<BR>X= -5.9146 Y= 11.0296 Z= 6.9595 Tot= 14.3202<BR>ONIOM: Integrating ONIOM file 5 number 695<BR>GetSCM: Allocation for LST2 failed:<BR>Core=-1707151352 Need=1090405693 GauSpace=-1707151352 MaxMem=52428800<BR>Avail=52428800.<BR>Error termination via Lnk1e in /local//g03/l107.exe at Wed Nov 29 00:07:52<BR>2006.<BR>Job cpu time: 0 days 13 hours 50 minutes 26.6 seconds.<BR>File lengths (MBytes): RWF= 468 Int= 0 D2E= 0 Chk= 167<BR>Scr= 1<BR><BR>[route card= # opt oniom(b3lyp/6-311++g(2d,p):am1:uff) geom=connectivity<BR>scf=xqc opt=loose ]<BR><BR>Has anyone else experienced this error?<BR>Any insight as to what is wrong is much appreciated.<BR>Al<BR><BR>------_=_NextPart_001_01C713C5.71DF1BB4<BR>Content-Type:
 text/html;<BR>charset="iso-8859-1"<BR>Content-Transfer-Encoding: quoted-printable<BR><BR><BR><BR><BR>  <META http-equiv='3D"Content-Type"' content='3D"text/html;' ="<br">charset=3Diso-8859-1"&gt;<BR>  <META content='3D"MS' name='3D"Generator"' version="<br" Server Exchange>5.5.2658.34"&gt;<BR><BR><BR><BR><BR>  <div><FONT size=3>Hi CCLers,</FONT><BR><BR><FONT size=3>I'm having trouble with a G03 ONIOM job which dies =<BR>after the following message:</FONT><BR></div><BR><BR>  <div><FONT size=3>...</FONT><BR><BR><FONT size=3>&nbsp;ONIOM: calculating electric field =<BR>derivatives.</FONT><BR><BR><FONT size=3>&nbsp;ONIOM: =<BR>Dipole&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =3D-2.32696873D+00 =<BR>4.33938853D+00 2.73808494D+00</FONT><BR><BR><FONT size=3>&nbsp;ONIOM: Dipole moment (Debye):</FONT><BR><BR><FONT size=3>&nbsp;&nbsp;&nbsp; X=3D&nbsp;&nbsp;&nbsp; =<BR>-5.9146&nbsp;&nbsp;&nbsp; Y=3D&nbsp;&nbsp;&nbsp; =<BR>11.0296&nbsp;&nbsp;&nbsp; Z=3D&nbsp;&nbsp;&nbsp;&nbsp;
 6.9595&nbsp; =<BR>Tot=3D&nbsp;&nbsp;&nbsp; 14.3202</FONT><BR><BR><FONT size=3>&nbsp;ONIOM: Integrating ONIOM file&nbsp; 5 =<BR>number&nbsp;&nbsp; 695</FONT><BR><BR><FONT size=3>GetSCM:&nbsp; Allocation for LST2&nbsp;&nbsp; =<BR>failed:</FONT><BR><BR><FONT size=3>Core=3D-1707151352 Need=3D1090405693 =<BR>GauSpace=3D-1707151352 MaxMem=3D52428800 Avail=3D52428800.</FONT><BR><BR><FONT size=3>&nbsp;Error termination via Lnk1e in =<BR>/local//g03/l107.exe at Wed Nov 29 00:07:52 2006.</FONT><BR><BR><FONT size=3>&nbsp;Job cpu time:&nbsp; 0 days 13 hours 50 minutes =<BR>26.6 seconds.</FONT><BR><BR><FONT size=3>&nbsp;File lengths (MBytes):&nbsp; =<BR>RWF=3D&nbsp;&nbsp;&nbsp; 468 Int=3D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 =<BR>D2E=3D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 Chk=3D&nbsp;&nbsp;&nbsp; 167 =<BR>Scr=3D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1</FONT><BR></div><BR><BR>  <div><FONT size=3>[route card=3D # opt =<BR>oniom(b3lyp/6-311++g(2d,p):am1:uff) geom=3Dconnectivity scf=3Dxqc =<BR>opt=3Dloose
 ]</FONT><BR></div><BR><BR>  <div><FONT size=3>Has anyone else experienced this error?</FONT><BR><BR><FONT size=3>Any insight as to what is wrong is much =<BR>appreciated.</FONT><BR><BR><FONT size=3>Al</FONT><BR></div><BR><BR><BR><BR>------_=_NextPart_001_01C713C5.71DF1BB4--<BR><BR><BR><BR<BR<BR<BR<BR><BR<BR>http://www.ccl.net/cgi-bin/ccl/send_ccl_message<BR><BR<BR>http://www.ccl.net/cgi-bin/ccl/send_ccl_message<BR><BR<BR>http://www.ccl.net/chemistry/sub_unsub.shtml<BR><BR<BR><BR<BR<BR><BR<BR><BR<BR>http://www.ccl.net/spammers.txt<BR><BR<BR><BR<BR><BR><BR><BR></BLOCKQUOTE><BR><p>&#32;__________________________________________________<br>Correo Yahoo!<br>Espacio para todos tus mensajes, antivirus y antispam ¡gratis! <br>Regístrate ya - http://correo.yahoo.com.mx/ 
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From owner-chemistry@ccl.net Fri Dec  1 04:19:01 2006
From: "Michel Petitjean ptitjean(!)itodys.jussieu.fr" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: A philosophical question for CCL'ers
Message-Id: <-33137-061201040750-14707-GNMRUcyRUaIRAk0WnAy9kw^_^server.ccl.net>
X-Original-From: Michel Petitjean <ptitjean]_[itodys.jussieu.fr>
Date: Fri, 1 Dec 2006 10:07:31 +0100 (MET)


Sent to CCL by: Michel Petitjean [ptitjean+/-itodys.jussieu.fr]
To: chemistry||ccl.net
Subject: CCL: Re: A philosophical question for CCL'ers

Eric Scerri wrote:
> Sodium a poisonous metal combines with chlorine, a greenish poisonous gas,
> to yield something that is not only non-poisonous but essential for life - NaCl.
> ...

Hope that most people don't confuse Na and Na+ or Cl2 with Cl-, etc.
I leave associated philosophical discussions for homeopaths, charlatans, ...

Michel Petitjean,                     Email: petitjean||itodys.jussieu.fr
ITODYS (CNRS, UMR 7086)                      ptitjean||ccr.jussieu.fr
1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.html


From owner-chemistry@ccl.net Fri Dec  1 09:16:01 2006
From: "lior itzhaki lior.itzhaki ~ gmail.com" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: Electrons' Density
Message-Id: <-33138-061129095147-22393-03zkX02sCN/U2QN1GCvfuw,server.ccl.net>
X-Original-From: "lior itzhaki" <lior.itzhaki#gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_28234_26881303.1164811903326"
Date: Wed, 29 Nov 2006 16:51:43 +0200
MIME-Version: 1.0


Sent to CCL by: "lior itzhaki" [lior.itzhaki],[gmail.com]

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 Dear CCLers,


I'm doing AB-initio calculation on a linear molecule (poly-acetylene).
Can anyone tell me how can I get the electrons' density as a function of the
distance from the main axis of the molecule?

Thank you
lior

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<span class="gmail_quote"></span>
<div>Dear CCLers,</div>
<div><br>&nbsp;</div>
<div>I'm doing AB-initio calculation on a linear molecule (poly-acetylene).</div>
<div>Can anyone&nbsp;tell me how can I get the electrons' density as a function of the distance from the main axis of the molecule?</div>
<div>&nbsp;</div>
<div>Thank you</div><span class="sg">
<div>lior</div>
<div>&nbsp;</div></span>

------=_Part_28234_26881303.1164811903326--


From owner-chemistry@ccl.net Fri Dec  1 09:50:00 2006
From: "matthew john tassell mtassell[#]gmail.com" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL:G: spin contamination
Message-Id: <-33139-061201092436-2648-Rxiz1FCJZOEgmbCqW6mPKQ[a]server.ccl.net>
X-Original-From: "matthew john tassell" <mtassell * gmail.com>
Date: Fri, 1 Dec 2006 09:24:35 -0500


Sent to CCL by: "matthew john tassell" [mtassell**gmail.com]
Dear all, im currently having a few problems with calculations not converging in G03 due to spin contamination. The system im looking at is AuXe4F2, and using cc style basis sets on all atoms with DFT. Iv tried Restricted Open Shell methodology as well with little success. A typical error message looks like this.

KE= 2.649085304160D+02 PE=-1.669013336414D+03 EE= 6.137794503227D+02
 Annihilation of the first spin contaminant:
 S**2 before annihilation     0.7500,   after     0.7500
 Convergence failure -- run terminated.
 Error termination via Lnk1e in /usr/local/g03/l502.exe at Fri Dec  1 13:58:00 2006.
 Job cpu time:  0 days  3 hours 41 minutes  3.7 seconds.
 File lengths (MBytes):  RWF=     59 Int=      0 D2E=      0 Chk=     10 Scr=      1

if you perhaps have any insight into this problem i would be very gratefull to hear from you, cheers, matt


From owner-chemistry@ccl.net Fri Dec  1 10:25:01 2006
From: "Yubo Fan yubofan(a)mail.chem.tamu.edu" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL: Amino Acid in Amber
Message-Id: <-33140-061130130124-24438-fSfG2QvFy/lvDJnqLzkWdA[]server.ccl.net>
X-Original-From: "Yubo Fan" <yubofan/./mail.chem.tamu.edu>
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Date: Thu, 30 Nov 2006 11:01:01 -0600
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Sent to CCL by: "Yubo Fan" [yubofan^_^mail.chem.tamu.edu]


This is a multi-part message in MIME format.

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Hi, Everyone,

I got problems to generate correct geometries for amino acids using =
AMBER. I mean I can generate correct structures for amono acid residues, =
including N-terminal, C-terminal and mid ones, BUT NOT a single amino =
acid such as alanine itself. Is there any way to generate the initial =
files for single amino acids from Amber force field? Thanks in advance.

Yubo Fan

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dr. Yubo Fan               Email: yubofan^mail.chem.tamu.edu
Department of Chemistry    Tel:   1-979-845-5237
Texas A&M University
College Station, TX 77843
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

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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=3Dgb2312">
<META content=3D"MSHTML 6.00.2900.2995" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Hi, Everyone,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I got problems to generate correct =
geometries for=20
amino acids using AMBER. I mean I can generate correct structures for =
amono acid=20
residues, including N-terminal, C-terminal and mid ones, BUT NOT a =
single amino=20
acid such as alanine itself. Is there any way to generate the initial =
files for=20
single amino acids from Amber force field? Thanks in =
advance.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Yubo Fan</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial=20
size=3D2>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<BR>Dr. Yubo=20
Fan&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;=20
Email: <A=20
href=3D"mailto:yubofan^mail.chem.tamu.edu">yubofan^mail.chem.tamu.edu</A>=
<BR>Department=20
of Chemistry&nbsp;&nbsp;&nbsp; Tel:&nbsp;&nbsp; 1-979-845-5237<BR>Texas =
A&amp;M=20
University<BR>College Station, TX=20
77843<BR>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV></BODY></HTML>

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From owner-chemistry@ccl.net Fri Dec  1 11:25:00 2006
From: "Daria Khvostichenko dkhvosti#uiuc.edu" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL:G: spin contamination
Message-Id: <-33141-061201112050-32116-g/hHM0zXYbU0/cDjQSbwcA%a%server.ccl.net>
X-Original-From: "Daria  Khvostichenko" <dkhvosti-*-uiuc.edu>
Date: Fri, 1 Dec 2006 11:20:50 -0500


Sent to CCL by: "Daria  Khvostichenko" [dkhvosti ~~ uiuc.edu]
Matthew,

Gaussian output makes it look like the issue is spin contamination, although in fact it is SCF convergence problem: SCF did not converge in the number of SCF cycles allowed (default is 128, I think). Normally SCF=XQC or SCF=QC would help. This topic has been discussed few times on CCL.

Daria


From owner-chemistry@ccl.net Fri Dec  1 12:12:00 2006
From: "Jeff Nauss jnauss=accelrys.com" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: Accelrys Customer Training for January 2007
Message-Id: <-33142-061201121041-23627-7EA6BptAazYmb+2Y0GGhaA _ server.ccl.net>
X-Original-From: Jeff Nauss <jnauss(-)accelrys.com>
Content-Type: text/plain; charset="US-ASCII"
Date: Fri, 1 Dec 2006 09:10:31 -0800
MIME-Version: 1.0


Sent to CCL by: Jeff Nauss [jnauss[-]accelrys.com]
Accelrys Inc. are holding the following training workshops during January 
2007.  These events are designed to help you get more value from your 
Accelrys software, helping you to better accomplish your research goals.

Costs for the scheduled workshops are $500 per day for all customers.  For 
the on-line presentations, the price is $175 per three hour session for 
all customers.


CAMBRIDGE, UK

Introduction to Polymer Modeling               23-24 Jan
Introduction to Quantum Mechanics Modeling     25-26 Jan
BTCL Scripting with Discover                   29 - 30 Jan
Nanomaterials Modeling                         31 Jan - 1 Feb
 
ONLINE TRAINING

Introduction to Material Studio                 16 Jan (4pm GMT)
Scripting with Materials Studio                 17 Jan (9am GMT) 
Introduction to Discovery Studio                30 Jan (4pm GMT) 
Pharmacophore Modeling with Discovery Studio    31 Jan (4pm GMT) 

Further details can be found on our website at 
http://www.accelrys.com/services/training/general/calendar.html
and 
http://www.accelrys.com/services/training/general/calendar_online.html.

Questions regarding scheduling and content should be directed to 
workshops{}accelrys.com

--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121-4779

Phone: +1-858-799-5555
Fax: +1-858-799-5100
http://www.accelrys.com/services/training/


From owner-chemistry@ccl.net Fri Dec  1 14:58:21 2006
From: "Anselm.Horn-*-chemie.uni-erlangen.de" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: Amino Acid in Amber
Message-Id: <-33144-061201120241-23124-HTvq3ZcMnh1jKJmpIghU0Q-,-server.ccl.net>
X-Original-From: Anselm.Horn{=}chemie.uni-erlangen.de
Content-Transfer-Encoding: 8bit
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Date: Fri, 1 Dec 2006 17:11:02 +0100 (CET)
MIME-Version: 1.0


Sent to CCL by: Anselm.Horn_._chemie.uni-erlangen.de
Hello,

> I got problems to generate correct geometries for amino acids using =
> AMBER. I mean I can generate correct structures for amono acid residues, =
> including N-terminal, C-terminal and mid ones, BUT NOT a single amino =
> acid such as alanine itself. Is there any way to generate the initial =
> files for single amino acids from Amber force field?
IMHO no, or better: not that easy. Remenber that the Amber program was
designed to treat proteins not single amino acids.

Of course, you could setup a new residue, that resembles the geometry and
charges of a single amino acid, but you'd have to create extra library
files for that; then you could select whether you wanted the zwitterionic
or the neutral form.

However, you should post that question on the Amber mailing list (check it's
archives first), as there might be a better solution, or someone has
already setup the parameter files.

Regards,

Anselm


From owner-chemistry@ccl.net Fri Dec  1 15:24:00 2006
From: "Jan Labanowski janl##speakeasy.net" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: Severe weather problems in MidOhio impacting CCL
Message-Id: <-33145-061201152137-15962-kojDgO2lmW5IPM8On9tkaA(0)server.ccl.net>
X-Original-From: "Jan Labanowski" <janl^speakeasy.net>
Content-Transfer-Encoding: 7bit
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Date: Fri, 01 Dec 2006 20:21:33 +0000
MIME-Version: 1.0


Sent to CCL by: "Jan Labanowski" [janl#speakeasy.net]
Dear CCL,
We do not have much luck lately with electricity...
The weather in Central Ohio is quite severe (very
strong winds) and many houses are without electricity
due to downed power lines. A few hours ago power went down
in my home ("the home of CCL" {:-|}). I learned that the
transformer blew up, so I powered down the CCL server that
was on UPS. Now the power is back but who knows for how long.
The network is also unstable. If you had sent a message to CCL
and it was not distributed, please ask me to look into
it or resend it. Sorry, but I really cannot do anything
about the acts of nature... So do not be surprised if
CCL goes down again in the near future... It is blowing
really good...

Jan Labanowski
CCL Manager
jkl|a|ccl.net


From owner-chemistry@ccl.net Fri Dec  1 15:33:38 2006
From: "errol lewars elewars ~ trentu.ca" <owner-chemistry*o*server.ccl.net>
To: CCL
Subject: CCL:G: Optimisation, flat rings and imag freqs
Message-Id: <-33146-061130112240-10998-jW4mtityKirPmvh88S6b9A*o*server.ccl.net>
X-Original-From: errol lewars <elewars_-_trentu.ca>
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Date: Thu, 30 Nov 2006 11:24:40 -0500
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Sent to CCL by: errol lewars [elewars~!~trentu.ca]

2006 Nov 30

This is addressed in:

D. Moran et al., J Am Chem Soc, 2006, 128(9), 9342.

E. Lewars
=============


zborowsk]_[chemia.uj.edu.pl wrote:

>Sent to CCL by: zborowsk**chemia.uj.edu.pl
>Hi
>and you ring is flat??
>I do not know exactly why but I observed many times that if DFT methods
>(especially when B3LYP is used) there is one imaginary frequency for
>planar structures while in HF calculations all frequencies is OK
>
>I am also want to know WHY
>
>any suggestions??
>
>  
>
>>Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi^^intnet.mu]
>>This is a multi-part message in MIME format.
>>
>>------=_NextPart_000_001F_01C713BB.07C399E0
>>Content-Type: text/plain;
>>	charset="iso-8859-1"
>>Content-Transfer-Encoding: quoted-printable
>>
>>Dear All
>>
>>I have a five membered ring, I am trying to optimise it using Gaussian =
>>03W.
>>I have been able to do it at HF level with no imaginary freq.
>>However when I use this optimised structure for a B3LYP optimisation, I =
>>am getting one imaginary frequency.
>>Can any suggest what is going wrong?
>>
>>Thanks
>>Ramasami
>>
>>------=_NextPart_000_001F_01C713BB.07C399E0
>>Content-Type: text/html;
>>	charset="iso-8859-1"
>>Content-Transfer-Encoding: quoted-printable
>>
>><!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>Dear All</FONT></DIV>
>><DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
>><DIV><FONT face=3DArial size=3D2>I have a five membered ring, I am =
>>trying to=20
>>optimise it using Gaussian 03W.</FONT></DIV>
>><DIV><FONT face=3DArial size=3D2>I have been able to do it at HF level =
>>with no=20
>>imaginary freq.</FONT></DIV>
>><DIV><FONT face=3DArial size=3D2>However when I use this optimised =
>>structure for a=20
>>B3LYP optimisation, I am getting one imaginary frequency.</FONT></DIV>
>><DIV><FONT face=3DArial size=3D2>Can any suggest what is going =
>>wrong?</FONT></DIV>
>><DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
>><DIV><FONT face=3DArial size=3D2>Thanks</FONT></DIV>
>><DIV><FONT face=3DArial size=3D2>Ramasami</FONT></DIV></BODY></HTML>
>>
>>------=_NextPart_000_001F_01C713BB.07C399E0-->
>>
>>
>>
>>    
>>
>
>
>  
>


From owner-chemistry@ccl.net Fri Dec  1 16:28:00 2006
From: "Gustavo Seabra gustavo.seabra^^^gmail.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL:G: spin contamination
Message-Id: <-33147-061201155313-1766-4hPUVTgXOF6FXrfBj3gHyA .. server.ccl.net>
X-Original-From: "Gustavo Seabra" <gustavo.seabra*gmail.com>
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
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Date: Fri, 1 Dec 2006 15:53:08 -0500
MIME-Version: 1.0


Sent to CCL by: "Gustavo Seabra" [gustavo.seabra(~)gmail.com]
On 12/1/06, matthew john tassell mtassell[#]gmail.com
<owner-chemistry++ccl.net> wrote:
> Sent to CCL by: "matthew john tassell" [mtassell**gmail.com]
> Dear all, im currently having a few problems with calculations not converging in G03 due to spin contamination. The system im looking at is AuXe4F2, and using cc style basis sets on all atoms with DFT. Iv tried Restricted Open Shell methodology as well with little success. A typical error message looks like this.
>
> KE= 2.649085304160D+02 PE=-1.669013336414D+03 EE= 6.137794503227D+02
>  Annihilation of the first spin contaminant:
>  S**2 before annihilation     0.7500,   after     0.7500
>  Convergence failure -- run terminated.
>  Error termination via Lnk1e in /usr/local/g03/l502.exe at Fri Dec  1 13:58:00 2006.
>  Job cpu time:  0 days  3 hours 41 minutes  3.7 seconds.
>  File lengths (MBytes):  RWF=     59 Int=      0 D2E=      0 Chk=     10 Scr=      1

This has nothing to do with spin contamination. Actually, your system
had **NO** spin contamination - notice that the numbers before and
after gaussian tries to eliminate spin contaminations are the same.
Those numbers are *NOT* spin contamination per se, but the expectation
valule of the S^2 operator, which for a siglet is exactly 0.75.

What you are seeing there is rather some SCF convergence failure. Try
adding a "P" as the first thing in your route card, to tell Gaussan to
generate extra information about the SCF procedure, like for example:

#P B3LYP/cc-pVTZ blah blah blah...
^^^^

HTH

Gustavo.


From owner-chemistry@ccl.net Fri Dec  1 19:58:01 2006
From: "John Bushnell bushnell[-]chem.ucsb.edu" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: GROMACS installation on Mac-OS
Message-Id: <-33148-061201195540-4198-/CHfpVkiIlGe7Xr2zdI6bg*server.ccl.net>
X-Original-From: John Bushnell <bushnell~~chem.ucsb.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Fri, 1 Dec 2006 15:46:37 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: John Bushnell [bushnell.]|[.chem.ucsb.edu]

First of all:  I have never used GROMACS, and have extremely little
experience using MacOS.  But this does sound strange.

The first thing I would do is use the "which" command to make
absolutely sure that you are running the command that you think
you are via your path.  Like this:

which pdb2gmx

Just a guess, but this is always a good thing to check before
chasing down ghosts...

     - John

On Thu, 30 Nov 2006, Ibrahim M. Moustafa I.moustafa*o*psu.edu wrote:

> Sent to CCL by: "Ibrahim M. Moustafa" [I.moustafa^-^psu.edu]
>
> Yea, it segfaults only when I don't type the whole path name and this
> is what is puzzling me!
> Whether is it is a bug or something else faulty....I can't tell!
>
>    If you get the chance to install GROMOCS on MacOS and managed to
> get around this, plz let me know!
>
>      Kind regards,
>       Ibrahim
>
> At 02:59 PM 11/30/2006, you wrote:
>> Sent to CCL by: "M. L. Dodson" [mldodson{=}houston.rr.com]
>> On Thursday 30 November 2006 11:40, Ibrahim M. Moustafa I.moustafa##psu.edu
>> wrote:
>>> Sent to CCL by: "Ibrahim M. Moustafa" [I.moustafa**psu.edu]
>>>
>>> Hi,
>>>
>>>    Thanks Dodson for your reply. Actually, the $GMSBIN was already
>>> sitting in the $PATH prentenv confirmed that.
>>>   As for the Segmentation fault error, it could be as you suggested!
>>> but if so, how does this related to the way I type the command?
>>> For the time being, I'm aliasing all the commands in $GMSBIN and it
>>> is working (at least for the demo)!.
>>>
>>>     As for Amber, unfortunately, I don't have access to download it
>>> for the time being....same for Charmm.
>>>
>>
>> Hmmm... I Guess I misunderstood you about the segfault.  Do you
>> mean it segfaults only when you DO NOT type the whole path name?
>> Or the other way around?  In either case, I do not understand why
>> it should make any difference unless the pdb2gmx program is using
>> its argv[0] (executable file name) variable for some purpose.  I
>> will shut up now as I know very little about GROMACS itself.  I
>> was just answering with general Unix information.  Segfaults can
>> happen for many different reasons.  My suggestion was based on an
>> earlier installation of GROMACS on (Intel) FreeBSD where I had the
>> precision mismatch problem.
>>
>> If you still can not get it to work after other people put in
>> their 2 cents, let me know, and I will try to install GROMACS on
>> my iBook G4 to see if I can debug the problem.  Should be really
>> funny to measure how much longer simulations take on the iBook :-)
>>
>> Both AMBER and CHARMM cost $$ as well (but are well worth it if
>> you qualify for the academic prices).
>>
>> Bud Dodson
>>
>>>     thanks for your time and help,
>>>
>>>       Ibrahim
>>>
>>> At 08:53 PM 11/29/2006, you wrote:
>>>> Sent to CCL by: "M. L. Dodson" [mldodson^houston.rr.com]
>>>> On Wednesday 29 November 2006 16:30, Ibrahim M. Moustafa ria2(a)psu.edu
>>>>
>>>> wrote:
>>>>> Sent to CCL by: "Ibrahim M. Moustafa" [ria2|a|psu.edu]
>>>>> Hi everybody,
>>>>>
>>>>>     Thanks Rick for your advice; but actually my Xcode was recently
>>>>> updated! I'm kind of figured out what was the problem which is: after
>>>>> installation and setting the variables I got an error message
>>>>> "Segmentation fault" when trying to issue any command...or trying the
>>>>> demo tutorial!
>>>>>   It appeared that my installation was fine (even my compilation was
>>>>> alright......in fact compilation resulted in a code that is much
>>>>> faster than the provided binary for Mac-OSX).
>>>>> I found the whole path is required to issue GROMACS' command to run
>>>>> any program; although, the variable $GMXBIN is already set in my
>>>>> .cshrc file. This has solved the problem, but still I don't
>>>>> understand why I can't run the programs (e.g. pdb2gmx) by just typing
>>>>> "pdb2gmx" in the xterm rather than typing "$GMXBIN/pdb2gmx" to make
>>>>> it working!! I'm not sure if this is a an OS problem or GROMACS
>>>>> problem! or something obvious that I'm missing! Any advice would be
>>>>> appreciated.
>>>>>
>>>>>     I haven't heard any comments regarding TINKER vs GROMACS as a
>>>>> modelling package! wish I can hear from someone though!
>>>>>
>>>>>    thanks,
>>>>>   Ibrahim
>>>>
>>>> Try issuing the command
>>>>
>>>> printenv PATH
>>>>
>>>> and look to see if the $GMXBIN directory is in your path.  The
>>>> behavior you describe indicates it is probably not there.  Fix
>>>> your .cshrc to include it, and your "full path problem" should go
>>>> away.  The seg fault problem may indicate that your have some
>>>> component(s) compiled for single precision and other components
>>>> compiled for double precision.  On FreeBSD (at least on Intel
>>>> architectures), this can be confusing at times.  GROMACS gets a
>>>> lot of its speed by running in single precision, whereas most
>>>> other MD packages are compiled for double precision.  In
>>>> particular, make sure the compiled precisions match for your
>>>> GROMACS and FFTW installations.
>>>>
>>>> As to your TINKER vs GROMACS question, I prefer AMBER and namd :-)
>>>>
>>>> Bud Dodson
>>>>
>>>>> At 12:22 AM 11/28/2006, you wrote:
>>>>>> Sent to CCL by: Rick Venable [venabler(_)nhlbi.nih.gov]
>>>>>> There can be issues with the gcc and g77 versions under MacOS X; in
>>>>>> particular, if you've kept up to date with OS patches, you may need
>>>>>> to download a newer version of the Xcode tools from the Apple
>>>>>> Developer site.
>>>>>>
>>>>>> I had some problems compiling CHARMM until I updated my Xcode tools.
>>>>>>
>>>>>> --
>>>>>> Rick Venable        29/500
>>>>>> Membrane Biophysics Section
>>>>>> NIH/NHLBI Lab. of Computational Biology
>>>>>> Bethesda, MD  20892-8014   U.S.A.
>>>>>> (301) 496-1905   venabler AT nhlbi*nih*gov
>>>>>>
>>>>>>> Sent to CCL by: "Ibrahim M. Moustafa" [ria2!=!psu.edu]
>>>>>>>
>>>>>>>    I have a limited experience in Molecular modelling of protein
>>>>>>> structures; I'd love to expand my experience in that direction.
>>>>>>> So, I have few questions for people with more experience in the
>>>>>>> field. I wanted to install GROMACS package on my Mac-OS 10.4
>>>>>>> according to the instructions on the GROMACS website.
>>>>>>>   First, I installed the FFTW source as instructed in the README
>>>>>>> file. Then, I installed the GROMACS binary for the MacOS-X 10.4.
>>>>>>> However, it did not work! I tried the examples provided with the
>>>>>>> package but I got "Segmentation faults"....nothing in the output.
>>>>>>> Just a blank pages while the script is running interactively.
>>>>>>> I tried to build the package myself from the source code; but
>>>>>>> again I got the same error message when running the examples'
>>>>>>> scripts! Presumably, my installation was not successful!
>>>>>>> even running the command pdb2gmx gives that error message
>>>>>>> "Segmentation fault"!!!--
>>>>
>>>> M. L. Dodson
>>>> Email:  mldodson-at-houston-dot-rr-dot-com
>>>> Phone:  eight_three_two-56_three-386_one--
>> M. L. Dodson
>> Email:  mldodson-at-houston-dot-rr-dot-com
>> Phone:  eight_three_two-56_three-386_one>
>
>
>


From owner-chemistry@ccl.net Fri Dec  1 20:57:01 2006
From: "Steve Bowlus chezbowlus a goldrush.com" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: A philosophical question for CCL'ers
Message-Id: <-33149-061201123251-18929-yWOzGPw9yPL7qoCuEGDOdg(-)server.ccl.net>
X-Original-From: Steve Bowlus <chezbowlus[]goldrush.com>
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Sent to CCL by: Steve Bowlus [chezbowlus|,|goldrush.com]

A long-standing joke (as long as I have been in this business) or 
condemnation of the abysmal general scientific knowledge in the US is 
the proportion of general chemistry students who identify sodium 
chloride as a green gas ...

A succinct statement of scientific purpose is "If you can't measure it, 
it is just your opinion."  Modelers provide "measurements" (whether 
statistical, static, or through dynamic simulation) ... or do these 
count as "measurement"?  In the early 90's, computational toxicology was 
impeded in teh ag chem industry by a US regulatory requirement that 
-all- adverse environmental events be disclosed.  Some corporations 
would not do any modeling in this area, since it was not known whether 
the result of a simulation by a validated method would be considered a 
reportable "event".

I realize that many people will classify regulatory agencies with 
charlatans, but these philosophical issues do impinge on how perceive 
our discipline and we do our jobs.

-Steve

> Eric Scerri wrote:
> 
>>Sodium a poisonous metal combines with chlorine, a greenish poisonous gas,
>>to yield something that is not only non-poisonous but essential for life - NaCl.
>>...
> 
> 
> Hope that most people don't confuse Na and Na+ or Cl2 with Cl-, etc.
> I leave associated philosophical discussions for homeopaths, charlatans, ...
> 
> Michel Petitjean,                     Email: petitjean=-=itodys.jussieu.fr
> ITODYS (CNRS, UMR 7086)                      ptitjean=-=ccr.jussieu.fr
> 1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
> 75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
> http://petitjeanmichel.free.fr/itoweb.petitjean.html
>


From owner-chemistry@ccl.net Fri Dec  1 21:56:00 2006
From: "N. Sukumar nagams_+_rpi.edu" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: A philosophical question for CCL'ers
Message-Id: <-33150-061201215106-30223-212JmnH0TzufYRRwBEyN/A(-)server.ccl.net>
X-Original-From: "N. Sukumar" <nagams+/-rpi.edu>
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Date: Fri, 01 Dec 2006 21:51:00 -0500
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Sent to CCL by: "N. Sukumar" [nagams^rpi.edu]
==============Original message text===============
On Fri, 01 Dec 2006 20:57:47 EST "Steve Bowlus chezbowlus a goldrush.com" 
wrote:

Sent to CCL by: Steve Bowlus [chezbowlus|,|goldrush.com]

> A long-standing joke (as long as I have been in this business) or 
condemnation of the abysmal general scientific knowledge in the US is the 
proportion of general chemistry students who identify sodium 
chloride as a green gas ...

> but these philosophical issues do impinge on how perceive our
discipline and we do our jobs.

-Steve

===========End of original message text===========

At a lecture several years ago, Phillip Martin Johnson of Stony Brook
threw out the statement, "Benzene is a greenish-yellow gas" to watch for
the audience's reaction. The statement is true, of course, if you're
talking about the multi-photon ionization spectrum, as Phil was (J. Chem. 
Phys. 64, 4143-4148 (1976)... Which just goes to show that what we
colloquially refer to as "properties" are often context-dependent and
environment-dependent. As we all know and acknowledge, the properties of
an atom in a molecule ("sodium" or "chlorine" in NaCl or "hydrogen" or
"oxygen" in water) depend upon its bonding environment; the properties of 
a molecule in vitro depend on the solvent and other conditions.

Can the properties of water be predicted from those of "hydrogen" and
"oxygen"? Yes, to a good approximation, as long we associate  these atom
types with the corresponding virial fragments in the bonding environment
found in water (rather than with those in H-H and O=O).

Dr. N. Sukumar
Rensselaer Exploratory Center for Cheminformatics Research
Center for Biotechnology and Interdisciplinary Studies
Rensselaer Polytechnic Institute
http://www.chem.rpi.edu/chemweb/recondoc/sukumar/http://reccr.chem.rpi.edu/


From owner-chemistry@ccl.net Fri Dec  1 22:30:01 2006
From: "Eric Scerri scerri**chem.ucla.edu" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL: thanks
Message-Id: <-33151-061201221235-19137-zIgGg+mGKfl+DFtBNHoIyQ::server.ccl.net>
X-Original-From: Eric Scerri <scerri(-)chem.ucla.edu>
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Date: Fri, 1 Dec 2006 19:18:11 -0800
Mime-Version: 1.0 (Apple Message framework v752.2)


Sent to CCL by: Eric Scerri [scerri-$-chem.ucla.edu]

--Apple-Mail-26--108785339
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Thanks for your posting but I have no idea of what you are getting at  
and how it might relate to the questions I asked!


eric scerri


------------------------------------------------------------------------ 
------------------------------------------------
The Periodic Table: Its Story and Its Significance, by Eric Scerri,  
Oxford University Press, 2006.

------------------------------------------------------------------------ 
------------------------------------------------
Dr. Eric Scerri,
Department of Chemistry & Biochemistry,
UCLA,
Los Angeles,
CA 90095-1569

E-mail scerri+/-chem.ucla.edu
Tel: 310 206 7443

UCLA faculty web page:   http://www.chem.ucla.edu/dept/Faculty/scerri/

Editor of Foundations of Chemistry,
http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- 
detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, 
00.html

International Society for the Philosophy of Chemistry,
http://ispc.sas.upenn.edu/






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questions I asked!<DIV><BR =
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class=3D"khtml-block-placeholder"></DIV><DIV>eric scerri</DIV><DIV><BR =
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"><DIV>-------------------------------------------------------------------=
-----------------------------------------------------</DIV></SPAN></SPAN><=
DIV><DIV>The Periodic Table: Its Story and Its Significance, by Eric =
Scerri, Oxford University Press, 2006.</DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>-----------------------------=
--------------------------------------------------------------------------=
-----------------</DIV><DIV>Dr. Eric Scerri,</DIV><DIV>Department of =
Chemistry &amp; Biochemistry,</DIV><DIV>UCLA,</DIV><DIV>Los =
Angeles,</DIV><DIV>CA 90095-1569</DIV><DIV><BR></DIV><DIV>E-mail <A =
href=3D"mailto:scerri+/-chem.ucla.edu">scerri+/-chem.ucla.edu</A></DIV><DIV>Te=
l: 310 206 7443</DIV><DIV><BR></DIV><DIV>UCLA faculty web page:=A0=A0=A0<A=
 =
href=3D"http://www.chem.ucla.edu/dept/Faculty/scerri/">http://www.chem.ucl=
a.edu/dept/Faculty/scerri/</A></DIV><DIV><BR></DIV><DIV>Editor of =
Foundations of Chemistry,</DIV><DIV><A =
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882-detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles,=
00.html">http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-3554=
5882-detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles=
,00.html</A></DIV><DIV><BR></DIV><DIV>International Society for the =
Philosophy of Chemistry,</DIV><DIV><A =
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