From owner-chemistry@ccl.net Mon Jul 28 10:56:01 2008
From: "Mahmoud Korani Abdel-Latif mkkhedr:-:hotmail.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL:G: TD-DFT
Message-Id: <-37430-080728044626-11838-sGUO2sZgdih+gQ+9RbyHhg:server.ccl.net>
X-Original-From: "Mahmoud Korani Abdel-Latif" <mkkhedr*_*hotmail.com>
Date: Mon, 28 Jul 2008 04:46:22 -0400
Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr[#]hotmail.com]
Dear All,
I am calculating TD-DFT using Gamess package But unfortunately There is Abnormal termination. Although the input I used is Gaussian output.
I am using the following basis set with B3LYP thepry.
$basis gbasis=N31 ngauss=6 diffsp=.T. ndfunc=1 npfunc=1 $end.
I got smething like in the output file:
THE INPUT BASIS SET CONTAINS APPROXIMATE LINEAR DEPENDENCE.
THE SMALLEST EIGENVALUE OF THE OVERLAP MATRIX IS 2.211503E-09
THERE ARE 19 EIGENVALUES LESS THAN QMTTOL= 1.00E-06
EIGENVECTORS BELOW -QMTTOL- ARE DROPPED FROM THE MO SPACE,
IN ORDER TO ELIMINATE THE APPROXIMATE LINEAR DEPENDENCE.
...... END OF TWO-ELECTRON INTEGRALS
SCF IS UNCONVERGED, TOO MANY ITERATIONS
TIME TO FORM FOCK OPERATORS= 187018.4 SECONDS ( 935.1 SEC/ITER)
FOCK TIME ON FIRST ITERATION= 1764.2, LAST ITERATION= 709.7
TIME TO SOLVE SCF EQUATIONS= 6727.9 SECONDS ( 33.6 SEC/ITER)
FINAL R-B3LYP ENERGY IS 0.0000000000 AFTER 200 ITERATIONS
DFT EXCHANGE + CORRELATION ENERGY = -196.7509056337
TOTAL ELECTRON NUMBER = 287.9994180225
...... END OF RHF CALCULATION ......
STEP CPU TIME =193774.12 TOTAL CPU TIME = 891689.4 (14861.5 MIN)
TOTAL WALL CLOCK TIME= 907324.0 SECONDS, CPU UTILIZATION IS 98.28%
SCF DID NOT CONVERGE...NO TDDFT=EXCITE CALCULATION
EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Mon Jul 28 05:32:46 2008
76515198 WORDS OF DYNAMIC MEMORY USED
Could you please tell me what should I do to overcome this problem.
Best regards,
Mahmoud Abdel-Latif,
mkkhedr(!)hotmail.com
From owner-chemistry@ccl.net Mon Jul 28 11:32:01 2008
From: "Mahmoud Korani Abdel-Latif mkkhedr : hotmail.com" <owner-chemistry()server.ccl.net>
To: CCL
Subject: CCL:G: TD/DFT
Message-Id: <-37431-080728045311-12457-t0SN11IkKZB+vxLvWcdWfg()server.ccl.net>
X-Original-From: "Mahmoud Korani Abdel-Latif" <mkkhedr(!)hotmail.com>
Date: Mon, 28 Jul 2008 04:53:07 -0400
Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr[]hotmail.com]
Dear All,
I am calculating TD-DFT using Gamess package But unfortunately There is Abnormal termination. Although the input I used is Gaussian output.
I am using the following basis set with B3LYP thepry.
$basis gbasis=N31 ngauss=6 diffsp=.T. ndfunc=1 npfunc=1 $end.
I got smething like in the output file:
THE INPUT BASIS SET CONTAINS APPROXIMATE LINEAR DEPENDENCE.
THE SMALLEST EIGENVALUE OF THE OVERLAP MATRIX IS 2.211503E-09
THERE ARE 19 EIGENVALUES LESS THAN QMTTOL= 1.00E-06
EIGENVECTORS BELOW -QMTTOL- ARE DROPPED FROM THE MO SPACE,
IN ORDER TO ELIMINATE THE APPROXIMATE LINEAR DEPENDENCE.
...... END OF TWO-ELECTRON INTEGRALS
SCF IS UNCONVERGED, TOO MANY ITERATIONS
TIME TO FORM FOCK OPERATORS= 187018.4 SECONDS ( 935.1 SEC/ITER)
FOCK TIME ON FIRST ITERATION= 1764.2, LAST ITERATION= 709.7
TIME TO SOLVE SCF EQUATIONS= 6727.9 SECONDS ( 33.6 SEC/ITER)
FINAL R-B3LYP ENERGY IS 0.0000000000 AFTER 200 ITERATIONS
DFT EXCHANGE + CORRELATION ENERGY = -196.7509056337
TOTAL ELECTRON NUMBER = 287.9994180225
...... END OF RHF CALCULATION ......
STEP CPU TIME =193774.12 TOTAL CPU TIME = 891689.4 (14861.5 MIN)
TOTAL WALL CLOCK TIME= 907324.0 SECONDS, CPU UTILIZATION IS 98.28%
SCF DID NOT CONVERGE...NO TDDFT=EXCITE CALCULATION
EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Mon Jul 28 05:32:46 2008
76515198 WORDS OF DYNAMIC MEMORY USED
Could you please tell me what should I do to overcome this problem.
Best regards,
Mahmoud Abdel-Latif,
mkkhedr_+_hotmail.com
From owner-chemistry@ccl.net Mon Jul 28 12:10:01 2008
From: "Shina Kamerlin skamerli ~ usc.edu" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL:G: Solvation Entropy
Message-Id: <-37432-080727140422-1508-HlZdbcaPVa10FZZnNwMJgg+/-server.ccl.net>
X-Original-From: Shina Kamerlin <skamerli:usc.edu>
Content-disposition: inline
Content-language: en
Content-transfer-encoding: 7BIT
Content-type: text/plain; charset=us-ascii
Date: Sun, 27 Jul 2008 10:18:08 -0700
MIME-version: 1.0
Sent to CCL by: Shina Kamerlin [skamerli_+_usc.edu]
Hi!
You can easily and pretty accurately estimate the solvation entropy using ChemSol:
http://futura.usc.edu/programs/index.html
For the configurational entropy, just use restraint release, as outlined in e.g.
Strajbl et al., Calculations of activation entropies of chemical reactions in solution, J. Phys. Chem. B. 104 (2000), 4578
This will give you the total entropy quite accurately.
Good luck!
Lynn
----- Original Message -----
> From: "Sebastian Kozuch kozuchs%a%yahoo.com" <owner-chemistry[#]ccl.net>
Date: Sunday, July 27, 2008 9:40 am
Subject: CCL:G: Solvation Entropy
To: "Kamerlin, Shina " <skamerli[#]usc.edu>
> Dear CCLers:
> Do someone know how to estimate the solvation entropy?
> Using gaussian you can easily calculate the solvation free energy
> of a molecule. On the other side, you can calculate the free energy
> in gas phase. But when doing free energy calculation (using freq
> keyword) in solvent, the entropy added is mostly the gas phase one,
> which adds a huge error, since the translational and rotational
> parts of the entropy are very different in solvent and gas phase.
> So what should be the best solution? Adding the solvation energy to
> the energy or to the free energy? Is there something more accurate?
>
> Thanks in advance,
>
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> ..........Sebastian Kozuch...........
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> ...The Lise Meitner-Minerva Center...
> .for Computational Quantum Chemistry.
> ...Hebrew University of Jerusalem....
> .....kozuchs]![yfaat.ch.huji.ac.il.....
> http://yfaat.ch.huji.ac.il/kozuch.htm
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>
>
>
>
From owner-chemistry@ccl.net Mon Jul 28 19:32:01 2008
From: "David Wild djwild]^[indiana.edu" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: CALL FOR PAPERS: eScience for Cheminformatics and Drug Discovery 2008 Workshop
Message-Id: <-37433-080728111741-4777-cQGx0Fwwm8GSjhWGszuO0g.@.server.ccl.net>
X-Original-From: David Wild <djwild(a)indiana.edu>
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Date: Mon, 28 Jul 2008 10:36:50 -0400
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Sent to CCL by: David Wild [djwild[#]indiana.edu]
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CALL FOR PAPERS: eScience for Cheminformatics and Drug Discovery
2008 Workshop
We are pleased to announce that we are now accepting abstracts of
papers for presentation at the eScience for Cheminformatics and Drug
Discovery Workshop 2008. This workshop will be held in conjunction
with the 4th IEEE International Conference on e-Science (e-Science
2008) in Indianapolis, Indiana, USA, December 7-12 2008.
Cheminformatics is becoming an increasingly important part of drug
discovery, chemistry, biology, toxicology and environmental science.
There are now huge volumes of information about chemical compounds
and their related biological properties available in the public
domain, as well as in proprietary databases, and a large number of
computations that can be applied to this information. There is thus
much interest in the application of eScience and cyberinfrastructure
to such information mining and computation problems. We are
requesting papers that will cover a variery of aspects of this
emerging application of eScience and grid computing in chemistry,
cheminformatics, biology, toxicology, environmental science and
computer-aided drug discovery. Papers should address one or more of
the following areas:
* Computation on extremely large chemical datasets (>10m
chemical structures)
* Distributed data mining of large chemical and biological datasets
* Grand challenges in cheminformatics
* High impact opportunities for cheminformatics and eScience
* Cloud computing infrastructure requirements for cheminformatics
* Chemistry-aware search engines and journal article processing
tools
* Natural Language Processing and Semantic Web applications
More information can be found on the conference website at http://
cheminfo.informatics.indiana.edu/eScience2008/ . Abstracts should be
submitted through the EasyChair site at http://www.easychair.org/
conferences/?conf=ecdd2008.
Please contact us with any questions
David Wild
Rajarshi Guha
Marlon Pierce
Workshop Organizers
___________________________________________
Dr. David J. Wild, djwild(~)indiana.edu
Assistant Professor of Informatics
Associate Director of Chemical Informatics
Indiana University School of Informatics
901 E. 10th St. Rm. 201A, Bloomington, IN 47408
ph (812) 856-1848 - fax (608) 541-5402 - web http://djwild.info
--Apple-Mail-286-577925712
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<html><body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; "><b>CALL FOR PAPERS: eScience =
for Cheminformatics and Drug Discovery 2008 =
=A0Workshop</b><div><br></div><div>We are pleased to announce that we =
are now accepting abstracts of papers for presentation at the =
<b>eScience for Cheminformatics and Drug Discovery Workshop 2008</b>. =
This workshop will be held in conjunction with the=A0<span =
class=3D"Apple-style-span" style=3D"font-family: Helvetica; ">4th IEEE =
International Conference on e-Science (e-Science 2008) in Indianapolis, =
Indiana, USA, December 7-12 2008.=A0</span></div><div><font =
class=3D"Apple-style-span" face=3D"Helvetica"><br></font></div><div><font =
class=3D"Apple-style-span" face=3D"Helvetica"><div style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
Helvetica">Cheminformatics is becoming an increasingly important part of =
drug discovery, chemistry, biology, toxicology and environmental =
science. There are now huge volumes of information about chemical =
compounds and their related biological properties available in the =
public domain, as well as in proprietary databases, and a large number =
of computations that can be applied to this information. There is thus =
much interest in the application of eScience and cyberinfrastructure to =
such information mining and computation problems. We are requesting =
papers that will cover a variery of aspects of this emerging application =
of eScience and grid computing in chemistry, cheminformatics, biology, =
toxicology, environmental science and computer-aided drug discovery. =
Papers should address one or more of the following =
areas:</font></div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; font: normal normal normal =
12px/normal Helvetica; min-height: 14px; "><br></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><font face=3D"Helvetica" size=3D"3" style=3D"font: =
12.0px Helvetica">=A0 =A0 * Computation on extremely large chemical =
datasets (>10m chemical structures)</font></div><div style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px Helvetica">=A0 =A0 * =
Distributed data mining of large chemical and biological =
datasets</font></div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; "><font face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica">=A0 =A0 * Grand challenges =
in cheminformatics</font></div><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px Helvetica">=A0 =A0 * =
High impact opportunities for cheminformatics and =
eScience</font></div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; "><font face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica">=A0 =A0 * Cloud computing =
infrastructure requirements for cheminformatics</font></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><font face=3D"Helvetica" size=3D"3" style=3D"font: =
12.0px Helvetica">=A0 =A0 * Chemistry-aware search engines and journal =
article processing tools</font></div><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px Helvetica">=A0 =A0 * =
Natural Language Processing and Semantic Web =
applications</font></div><div style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">More information can be found on the conference =
website at=A0<a =
href=3D"http://cheminfo.informatics.indiana.edu/eScience2008/">http://chem=
info.informatics.indiana.edu/eScience2008/</a>=A0<span =
class=3D"Apple-style-span" style=3D"font-family: 'Lucida Grande'; ">. =
Abstracts should be submitted through the EasyChair site at=A0<span =
class=3D"Apple-style-span" style=3D"font-family: Helvetica; "><a =
href=3D"http://www.easychair.org/conferences/?conf=3Decdd2008">http://www.=
easychair.org/conferences/?conf=3Decdd2008</a><span =
class=3D"Apple-style-span" style=3D"font-family: 'Lucida Grande'; =
">.</span></span></span></div><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font =
class=3D"Apple-style-span" face=3D"'Lucida =
Grande'"><br></font></div><div style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; "><span =
class=3D"Apple-style-span" style=3D"font-family: 'Lucida Grande'; =
"><span class=3D"Apple-style-span" style=3D"font-family: Helvetica; =
"><span class=3D"Apple-style-span" style=3D"font-family: 'Lucida =
Grande'; ">Please contact us with any =
questions</span></span></span></div><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font =
class=3D"Apple-style-span" face=3D"'Lucida =
Grande'"><br></font></div><div style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; "><span =
class=3D"Apple-style-span" style=3D"font-family: 'Lucida Grande'; =
"><span class=3D"Apple-style-span" style=3D"font-family: Helvetica; =
"><span class=3D"Apple-style-span" style=3D"font-family: 'Lucida =
Grande'; ">David Wild</span></span></span></div><div style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span =
class=3D"Apple-style-span" style=3D"font-family: 'Lucida Grande'; =
"><span class=3D"Apple-style-span" style=3D"font-family: Helvetica; =
"><span class=3D"Apple-style-span" style=3D"font-family: 'Lucida =
Grande'; ">Rajarshi Guha</span></span></span></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><span class=3D"Apple-style-span" style=3D"font-family:=
'Lucida Grande'; "><span class=3D"Apple-style-span" style=3D"font-family:=
Helvetica; "><span class=3D"Apple-style-span" style=3D"font-family: =
'Lucida Grande'; ">Marlon Pierce</span></span></span></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><font class=3D"Apple-style-span" face=3D"'Lucida =
Grande'"><br></font></div><div style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; "><font =
class=3D"Apple-style-span" face=3D"'Lucida Grande'">Workshop =
Organizers</font></div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; "><span class=3D"Apple-style-span" =
style=3D"font-family: 'Lucida Grande'; "><span class=3D"Apple-style-span" =
style=3D"font-family: Helvetica; "><span class=3D"Apple-style-span" =
style=3D"font-family: 'Lucida Grande'; =
">=A0</span></span></span></div></font><div> <span =
class=3D"Apple-style-span" style=3D"border-collapse: separate; color: =
rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: 12px; font-style: =
normal; font-variant: normal; font-weight: normal; letter-spacing: =
normal; line-height: normal; orphans: 2; text-align: auto; text-indent: =
0px; text-transform: none; white-space: normal; widows: 2; word-spacing: =
0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
'Lucida Grande'; font-size: 12px; font-style: normal; font-variant: =
normal; font-weight: normal; letter-spacing: normal; line-height: =
normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: =
normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: =
0px; -webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; -webkit-border-horizontal-spacing: =
0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); =
font-family: 'Lucida Grande'; font-size: 12px; font-style: normal; =
font-variant: normal; font-weight: normal; letter-spacing: normal; =
line-height: normal; -webkit-text-decorations-in-effect: none; =
text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; =
orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><div><div style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; "><div style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; =
">___________________________________________</div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; min-height: 14px; "><br></div><div style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dr. =
David J. Wild, <a =
href=3D"mailto:djwild(~)indiana.edu">djwild(~)indiana.edu</a></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Assistant Professor of Informatics</div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">Associate Director of Chemical =
Informatics</div></div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; min-height: 14px; ">Indiana =
University School of Informatics<br></div><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
14px; ">901 E. 10th St. Rm. 201A, Bloomington, IN 47408</div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">ph (812) 856-1848 - fax=A0(608) 541-5402=A0-=A0web =
<a =
href=3D"http://djwild.info">http://djwild.info</a></div></div></div></div>=
</div></span></span></span> </div><br></div></body></html>=
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