From owner-chemistry@ccl.net Wed Aug 26 07:41:00 2015
From: "Grigoriy Zhurko reg_zhurko*chemcraftprog.com" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL:G: Mixed basis sets and Gaussian
Message-Id: <-51617-150826025943-30408-F/uVqgNuQaUw/nW5RsDuWA~!~server.ccl.net>
X-Original-From: Grigoriy Zhurko <reg_zhurko.:.chemcraftprog.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=koi8-r
Date: Wed, 26 Aug 2015 10:59:42 +0400
MIME-Version: 1.0
Sent to CCL by: Grigoriy Zhurko [reg_zhurko+/-chemcraftprog.com]
Hello,
1) I didn�t yet find, how to specify in Gaussian individual basis sets for individual atoms in molecule (not for atom types).
Usually, in the Gaussian samples, when the GEN keyword is used for typing the basis set, below the atomic coordinates the basis sets for each atom type in molecule are typed, e.g.:
#P CCSD/Gen Scan Test scf=(nosymm,xqc) geom=nocrowd
Gaussian Test Job 467:
Li2 PES SCAN LOWEST TRIPLE CONFIGURATION
0 3
Li
Li,1,r1
r1=0.25 S 15 0.5
LI 0
S 5 1.00
1359.44660000 0.00084400
204.02647000 0.00648600
46.54954100 0.03247700
13.23259400 0.11742000
4.28614800 0.29458000
S 2 1.00
1.49554200 0.44951500
0.54223800 0.54223800
S 1 1.00
0.07396800 1.00000000
S 1 1.00
0.02809500 1.00000000
S 1 1.00
0.01067100 1.00000000
P 4 1.00
4.17000000 0.00511200
1.17256000 0.02090700
0.32927000 0.09167200
0.09271000 0.44926000
P 1 1.00
0.02607000 1.00000000
P 1 1.00
0.00733100 1.00000000
D 2 1.00
0.32927000 0.15975700
0.09271000 1.47548400
D 2 1.00
0.02607000 0.37057800
0.00733100 0.01784700
I have the bilirubin molecule, which has internal hydrogen bonds:
%MEM=700MB
%CHK=BR.chk
#P B3LYP/6-311++G(D,P) NMR
BR
0,1
6 4.942713000 0.701675000 1.334793000
6 5.518244000 -0.371321000 2.150333000
6 4.927502000 -1.550798000 1.760207000
6 3.954274000 -1.254693000 0.701347000
6 3.107310000 -2.119939000 0.073773000
6 2.064366000 -1.879342000 -0.873642000
6 1.227635000 -2.831893000 -1.478818000
6 0.302362000 -2.136680000 -2.307803000
6 0.605887000 -0.778424000 -2.204754000
6 0.035704000 0.446520000 -2.875397000
6 -0.548405000 1.468044000 -1.931383000
6 -0.248075000 2.811098000 -1.694482000
6 -1.186550000 3.281500000 -0.734241000
6 -2.028092000 2.208787000 -0.391789000
6 -3.082221000 2.213184000 0.570747000
6 -3.934134000 1.222819000 0.968717000
6 -4.912072000 1.264817000 2.044400000
6 -5.509051000 0.028016000 2.150788000
6 -4.916892000 -0.836627000 1.113225000
1 3.634017000 0.669225000 -0.260199000
7 4.025823000 0.120065000 0.499740000
7 1.653687000 -0.643250000 -1.344122000
7 -1.606210000 1.125300000 -1.144817000
7 -3.986855000 -0.075120000 0.457813000
1 2.048448000 0.264442000 -1.140201000
1 -3.591315000 -0.426508000 -0.409745000
8 5.184757000 1.922675000 1.358029000
8 -5.151789000 -2.024282000 0.827830000
6 0.821790000 3.635627000 -2.363400000
1 1.305672000 3.048643000 -3.146794000
1 0.354884000 4.488670000 -2.870103000
6 -1.277241000 4.677455000 -0.190844000
1 -0.999493000 5.413624000 -0.950118000
1 -2.291364000 4.921607000 0.132200000
1 -0.615333000 4.832687000 0.669093000
6 1.909517000 4.201916000 -1.432312000
1 2.548926000 4.897308000 -1.989819000
1 1.486241000 4.786839000 -0.613566000
6 2.834406000 3.166539000 -0.833920000
8 2.900203000 2.015790000 -1.259160000
8 3.566598000 3.630220000 0.154649000
1 4.198538000 2.942471000 0.553231000
6 1.309645000 -4.319142000 -1.294680000
1 2.317803000 -4.639911000 -1.024729000
1 0.632303000 -4.679319000 -0.511558000
1 1.045248000 -4.843594000 -2.217006000
6 -0.758818000 -2.767132000 -3.172819000
1 -1.234401000 -2.002543000 -3.790651000
1 -0.286216000 -3.468603000 -3.870612000
6 -1.857026000 -3.543899000 -2.423767000
1 -2.493081000 -4.072531000 -3.144436000
1 -1.443555000 -4.318573000 -1.775457000
6 -2.785054000 -2.687726000 -1.592778000
8 -3.517685000 -3.380854000 -0.749122000
8 -2.855092000 -1.468123000 -1.723911000
1 -4.152750000 -2.812401000 -0.198633000
1 3.219354000 -3.161267000 0.346353000
1 -3.204379000 3.159500000 1.081777000
1 -0.736115000 0.129370000 -3.582530000
6 6.520872000 -0.086314000 3.217995000
1 6.492491000 0.974649000 3.473144000
1 6.327250000 -0.675502000 4.118888000
1 7.541960000 -0.313763000 2.890035000
6 5.125530000 -2.893940000 2.291577000
1 4.317277000 -3.596805000 2.110105000
1 -6.837754000 -2.384504000 2.518395000
6 6.193745000 -3.341254000 2.964526000
1 6.231887000 -4.365115000 3.317296000
1 7.059266000 -2.724341000 3.167078000
1 0.818751000 0.928464000 -3.467641000
1 -2.004995000 0.196903000 -1.179742000
6 -5.196485000 2.460133000 2.901392000
1 -4.490839000 3.271748000 2.723362000
1 -6.202126000 2.848494000 2.710080000
1 -5.143102000 2.205642000 3.963542000
6 -6.524439000 -0.371530000 3.105599000
1 -6.831801000 0.400137000 3.807390000
6 -7.101766000 -1.579689000 3.191935000
1 -7.853832000 -1.774255000 3.947599000
As far as I know, hydrogen bonds require diffuse functions. How can I create an input file with this molecule, where most atoms have the 6-311G(D,P) basis set, and atoms 20,40, 27, 42, 25, etc (involved in H-bonds) have the 6-311++G(D,P) basis set?
2) A close question � can a Gaussian user type # GEN and specify the built-in basis sets below the atomic coordinates, not the full basis set description (with exponents/contraction coefficients)? I mean, that for my bilirubin molecule I don�t need the non-standard basis set, I just need 6-311G(D,P) on most atoms and 6-311++G(D,P) on some.
3) And a general question � is such approach (mixed, non-balanced basis set) correct? Maybe, some errors like BSSE may arise if I use such mixed basis sets? Maybe if I have a conjugated system and I specify stronger basis set on some its part, the electronic density will �spill over� into this part so the computation becomes incorrect?
From owner-chemistry@ccl.net Wed Aug 26 08:16:00 2015
From: "Violeta Isabel Perez Nueno violeta.pereznueno%loria.fr" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: CALL FOR PAPERS CINF symposium ACS San Diego 13-17 March 2016
Message-Id: <-51618-150826034548-6960-ftJKOUwlFLBFyDKJ/RP3bg+*+server.ccl.net>
X-Original-From: "Violeta Isabel Perez Nueno" <violeta.pereznueno^^loria.fr>
Date: Wed, 26 Aug 2015 03:45:46 -0400
Sent to CCL by: "Violeta Isabel Perez Nueno" [violeta.pereznueno%x%loria.fr]
*******************************************************************************************************
**************************************************************************
CALL FOR PAPERS Upcoming ACS Meeting Computers in Chemistry" , San Diego, California, March
13-17, 2016
DEADLINE ABSTRACT SUBMISSION: October 5th, 2015
*******************************************************************************************************
**************************************************************************
It is a great pleasure to announce the 251st ACS National Meeting & Exposition Theme : "Computers
in Chemistry", which will take place in San Diego in March 13-17, 2016.
On behalf of the CINF Programming Committee for ACS Meeting, I encourage you to submit your
abstracts to our CINF symposia, especially the symposium which I am organizing:
"Towards the integration of Quantitative and Systems Pharmacology into drug discovery: a systems
level understanding of therapeutic and toxic effects of drugs", cosponsored by MEDI and TOXI ACS
divisions
http://www.acs.org/content/acs/en/meetings/abstract-submissions/acsnm251/division-of-
chemical-information.html
Brief description of the symposium:
Over the past three decades, the predominant paradigm in drug discovery was designing selective
ligands for a specific target to avoid unwanted side effects. However, in the last 5 years, the aim has
shifted to take into account the biological network in which they interact. Quantitative and Systems
Pharmacology (QSP) is a new paradigm that aims to understand how drugs modulate cellular networks
in space and time, in order to predict drug targets and their role in human pathophysiology.
The goal of this symposium is to go trough the current computational and experimental QSP
approaches such as polypharmacology techniques combined with systems biology information and
consider the use of new tools and ideas in a wider 'systems-level' context in order to design new
drugs with improved efficacy and fewer unwanted off-target effects.
Abstracts may be submitted via the ACS online Program & Abstract Creation System (PACS) at:
https://acsmaps.abstractcentral.com/members/client/acs.jsp. You do not have to be an ACS member
to create an account for PACS (although if you have a login for the ACS site, you can use that). PACS is
open for abstract submissions and it will close to authors on October 5th 2016 for CINF Division. You
can learn more about American Chemical Society Meetings by visiting the website
http://www.acs.org/content/acs/en/meetings.html
Please do not hesitate to contact me if you have any questions. I look forward to hearing from you and
hope you can join us in San Diego in March 2016!
Best regards,
Violeta Isabel Perez Nueno
============================================================
E: violeta.pereznueno^-^loria.fr
Senior Researcher
T: +33 6 38 87 85 47
P: LORIA, INRIA Nancy Grand Est
Campus Scientifique, BP239
54506 Vandoeuvre-les-Nancy
France
W: http://www.loria.fr/~pereznue/
============================================================
From owner-chemistry@ccl.net Wed Aug 26 09:21:01 2015
From: "Mohammad Goodarzi mohammad.godarzi()gmail.com" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: peptides geometry optimization
Message-Id: <-51619-150826090039-20432-+gA8Eam0qFCSFnFgsNmH1Q . server.ccl.net>
X-Original-From: "Mohammad Goodarzi" <mohammad.godarzi*|*gmail.com>
Date: Wed, 26 Aug 2015 09:00:38 -0400
Sent to CCL by: "Mohammad Goodarzi" [mohammad.godarzi++gmail.com]
Hello,
I have a general question and I would like to know your thought in a
details way. I am looking to find a way to optimize the geometry of
peptides with different sizes. I don't have a supercomputer so I need a
simple, rather accurate way to do it (i know this is the dream of having
such software, I mean with a good accuracy) however, the speed is very
important for me because with hyperchem it takes like forever.
So, I need a way to find the best conformer of a peptide and then optimize
it geometry.
Any suggestion is welcome
Best Regards,
Mohammad
From owner-chemistry@ccl.net Wed Aug 26 10:44:00 2015
From: "Kraemer, Tobias T.Kraemer__hw.ac.uk" <owner-chemistry!A!server.ccl.net>
To: CCL
Subject: CCL:G: Mixed basis sets and Gaussian
Message-Id: <-51620-150826091156-14945-nyLsWK86zf6yHin+yjOKHQ!A!server.ccl.net>
X-Original-From: "Kraemer, Tobias" <T.Kraemer,,hw.ac.uk>
Content-Language: en-US
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset="koi8-r"
Date: Wed, 26 Aug 2015 13:11:00 +0000
MIME-Version: 1.0
Sent to CCL by: "Kraemer, Tobias" [T.Kraemer/a\hw.ac.uk]
Dear Grigoriy,
If I am not mistaken I think you can assign basis sets to individual atoms by referring to their specific numbering from the molecule specification list,
Instead of specifying the atom type one would specify
20,40,27,42,25 0
6-311++G(D,P)
****
and so forth. I think you can specify ranges of numbers as well (xx-yy), which should save you some time. There is one example on the Gaussian webpage for the Gen keyword, which can be easily missed, which shows how to place a diffuse function on one specific centre. Regarding you second question, yes, you can use the generic description of the basis set, as long as the it is stored internally and recognised by Gaussian (check the webpage). Gaussian is able to handle both formats (explicit with exponents and coefficients, and shorthand notation).
Using such a split basis approach is quite common. In your case, augmenting your basis set by diffuse functions on selected atoms involved in hydrogen bonding should not alter the overall electronic structure of the full molecule notably. After all you are still using basis sets of same triple-zeta quality on all atoms.
Best
Tobias
Dr. Tobias Kraemer MRSC
Research Associate
Institute of Chemical Sciences
School of Engineering & Physical Sciences
Heriot-Watt University
Edinburgh EH14 4AS
United Kingdom
email: t.kraemer{}hw.ac.uk
phone: +44 (0)131 451 3259
-----Original Message-----
> From: owner-chemistry+t.kraemer==hw.ac.uk{}ccl.net [mailto:owner-chemistry+t.kraemer==hw.ac.uk{}ccl.net] On Behalf Of Grigoriy Zhurko reg_zhurko*chemcraftprog.com
Sent: 26 August 2015 08:00
To: Kraemer, Tobias
Subject: CCL:G: Mixed basis sets and Gaussian
Sent to CCL by: Grigoriy Zhurko [reg_zhurko+/-chemcraftprog.com] Hello,
1) I didn�t yet find, how to specify in Gaussian individual basis sets for individual atoms in molecule (not for atom types).
Usually, in the Gaussian samples, when the GEN keyword is used for typing the basis set, below the atomic coordinates the basis sets for each atom type in molecule are typed, e.g.:
#P CCSD/Gen Scan Test scf=(nosymm,xqc) geom=nocrowd
Gaussian Test Job 467:
Li2 PES SCAN LOWEST TRIPLE CONFIGURATION
0 3
Li
Li,1,r1
r1=0.25 S 15 0.5
LI 0
S 5 1.00
1359.44660000 0.00084400
204.02647000 0.00648600
46.54954100 0.03247700
13.23259400 0.11742000
4.28614800 0.29458000
S 2 1.00
1.49554200 0.44951500
0.54223800 0.54223800
S 1 1.00
0.07396800 1.00000000
S 1 1.00
0.02809500 1.00000000
S 1 1.00
0.01067100 1.00000000
P 4 1.00
4.17000000 0.00511200
1.17256000 0.02090700
0.32927000 0.09167200
0.09271000 0.44926000
P 1 1.00
0.02607000 1.00000000
P 1 1.00
0.00733100 1.00000000
D 2 1.00
0.32927000 0.15975700
0.09271000 1.47548400
D 2 1.00
0.02607000 0.37057800
0.00733100 0.01784700
I have the bilirubin molecule, which has internal hydrogen bonds:
%MEM=700MB
%CHK=BR.chk
#P B3LYP/6-311++G(D,P) NMR
BR
0,1
6 4.942713000 0.701675000 1.334793000
6 5.518244000 -0.371321000 2.150333000
6 4.927502000 -1.550798000 1.760207000
6 3.954274000 -1.254693000 0.701347000
6 3.107310000 -2.119939000 0.073773000
6 2.064366000 -1.879342000 -0.873642000
6 1.227635000 -2.831893000 -1.478818000
6 0.302362000 -2.136680000 -2.307803000
6 0.605887000 -0.778424000 -2.204754000
6 0.035704000 0.446520000 -2.875397000
6 -0.548405000 1.468044000 -1.931383000
6 -0.248075000 2.811098000 -1.694482000
6 -1.186550000 3.281500000 -0.734241000
6 -2.028092000 2.208787000 -0.391789000
6 -3.082221000 2.213184000 0.570747000
6 -3.934134000 1.222819000 0.968717000
6 -4.912072000 1.264817000 2.044400000
6 -5.509051000 0.028016000 2.150788000
6 -4.916892000 -0.836627000 1.113225000
1 3.634017000 0.669225000 -0.260199000
7 4.025823000 0.120065000 0.499740000
7 1.653687000 -0.643250000 -1.344122000
7 -1.606210000 1.125300000 -1.144817000
7 -3.986855000 -0.075120000 0.457813000
1 2.048448000 0.264442000 -1.140201000
1 -3.591315000 -0.426508000 -0.409745000
8 5.184757000 1.922675000 1.358029000
8 -5.151789000 -2.024282000 0.827830000
6 0.821790000 3.635627000 -2.363400000
1 1.305672000 3.048643000 -3.146794000
1 0.354884000 4.488670000 -2.870103000
6 -1.277241000 4.677455000 -0.190844000
1 -0.999493000 5.413624000 -0.950118000
1 -2.291364000 4.921607000 0.132200000
1 -0.615333000 4.832687000 0.669093000
6 1.909517000 4.201916000 -1.432312000
1 2.548926000 4.897308000 -1.989819000
1 1.486241000 4.786839000 -0.613566000
6 2.834406000 3.166539000 -0.833920000
8 2.900203000 2.015790000 -1.259160000
8 3.566598000 3.630220000 0.154649000
1 4.198538000 2.942471000 0.553231000
6 1.309645000 -4.319142000 -1.294680000
1 2.317803000 -4.639911000 -1.024729000
1 0.632303000 -4.679319000 -0.511558000
1 1.045248000 -4.843594000 -2.217006000
6 -0.758818000 -2.767132000 -3.172819000
1 -1.234401000 -2.002543000 -3.790651000
1 -0.286216000 -3.468603000 -3.870612000
6 -1.857026000 -3.543899000 -2.423767000
1 -2.493081000 -4.072531000 -3.144436000
1 -1.443555000 -4.318573000 -1.775457000
6 -2.785054000 -2.687726000 -1.592778000
8 -3.517685000 -3.380854000 -0.749122000
8 -2.855092000 -1.468123000 -1.723911000
1 -4.152750000 -2.812401000 -0.198633000
1 3.219354000 -3.161267000 0.346353000
1 -3.204379000 3.159500000 1.081777000
1 -0.736115000 0.129370000 -3.582530000
6 6.520872000 -0.086314000 3.217995000
1 6.492491000 0.974649000 3.473144000
1 6.327250000 -0.675502000 4.118888000
1 7.541960000 -0.313763000 2.890035000
6 5.125530000 -2.893940000 2.291577000
1 4.317277000 -3.596805000 2.110105000
1 -6.837754000 -2.384504000 2.518395000
6 6.193745000 -3.341254000 2.964526000
1 6.231887000 -4.365115000 3.317296000
1 7.059266000 -2.724341000 3.167078000
1 0.818751000 0.928464000 -3.467641000
1 -2.004995000 0.196903000 -1.179742000
6 -5.196485000 2.460133000 2.901392000
1 -4.490839000 3.271748000 2.723362000
1 -6.202126000 2.848494000 2.710080000
1 -5.143102000 2.205642000 3.963542000
6 -6.524439000 -0.371530000 3.105599000
1 -6.831801000 0.400137000 3.807390000
6 -7.101766000 -1.579689000 3.191935000
1 -7.853832000 -1.774255000 3.947599000
As far as I know, hydrogen bonds require diffuse functions. How can I create an input file with this molecule, where most atoms have the 6-311G(D,P) basis set, and atoms 20,40, 27, 42, 25, etc (involved in H-bonds) have the 6-311++G(D,P) basis set?
2) A close question � can a Gaussian user type # GEN and specify the built-in basis sets below the atomic coordinates, not the full basis set description (with exponents/contraction coefficients)? I mean, that for my bilirubin molecule I don�t need the non-standard basis set, I just need 6-311G(D,P) on most atoms and 6-311++G(D,P) on some.
3) And a general question � is such approach (mixed, non-balanced basis set) correct? Maybe, some errors like BSSE may arise if I use such mixed basis sets? Maybe if I have a conjugated system and I specify stronger basis set on some its part, the electronic density will �spill over� into this part so the computation becomes incorrect?http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-----
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From owner-chemistry@ccl.net Wed Aug 26 11:20:00 2015
From: "John McKelvey jmmckel||gmail.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: peptides geometry optimization
Message-Id: <-51621-150826104125-1888-+GhX4eaWQ3iMthEwCRFPIQ**server.ccl.net>
X-Original-From: John McKelvey <jmmckel]*[gmail.com>
Content-Type: multipart/alternative; boundary=047d7b2e148d074e5b051e37d836
Date: Wed, 26 Aug 2015 09:41:19 -0500
MIME-Version: 1.0
Sent to CCL by: John McKelvey [jmmckel{}gmail.com]
--047d7b2e148d074e5b051e37d836
Content-Type: text/plain; charset=UTF-8
Mohammed,
An free code that can be very efficient is ORCA. It runs parallel on both
Windows and Linux machines with the appropriate hardware. It also can run
efficiently on a single core machine. It can handle many types of basis
sets, with many being built in.
Hope this helps.
John
On Wednesday, August 26, 2015, Mohammad Goodarzi mohammad.godarzi()gmail.com
<owner-chemistry * ccl.net> wrote:
>
> Sent to CCL by: "Mohammad Goodarzi" [mohammad.godarzi++gmail.com]
> Hello,
>
> I have a general question and I would like to know your thought in a
> details way. I am looking to find a way to optimize the geometry of
> peptides with different sizes. I don't have a supercomputer so I need a
> simple, rather accurate way to do it (i know this is the dream of having
> such software, I mean with a good accuracy) however, the speed is very
> important for me because with hyperchem it takes like forever.
>
> So, I need a way to find the best conformer of a peptide and then optimize
> it geometry.
>
> Any suggestion is welcome
> Best Regards,
> Mohammad>
> E-mail to subscribers: CHEMISTRY * ccl.net <javascript:;> or use:>
> E-mail to administrators: CHEMISTRY-REQUEST * ccl.net <javascript:;> or use>
>
>
--
John McKelvey
545 Legacy Pointe Dr
O'Fallon, MO 63376
636-294-5302
jmmckel * gmail.com
--047d7b2e148d074e5b051e37d836
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable
Mohammed,<div><br></div><div>An free=C2=A0code that can be very efficient i=
s ORCA.=C2=A0 It runs parallel on both Windows and Linux machines with the =
appropriate hardware.=C2=A0 It also can run efficiently on a single core ma=
chine.=C2=A0 It can handle many types of basis sets, with many being=C2=A0b=
uilt in.</div><div><br></div><div>Hope this helps.</div><div><br></div><div=
>John<br><br>On Wednesday, August 26, 2015, Mohammad Goodarzi mohammad.goda=
rzi()<a href=3D"http://gmail.com">gmail.com</a> <<a href=3D"mailto:owner=
-chemistry * ccl.net">owner-chemistry * ccl.net</a>> wrote:<br><blockquote c=
lass=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;=
padding-left:1ex"><br>
Sent to CCL by: "Mohammad=C2=A0 Goodarzi" [mohammad.godarzi++<a h=
ref=3D"http://gmail.com" target=3D"_blank">gmail.com</a>]<br>
Hello,<br>
<br>
I have a general question and I would like to know your thought in a<br>
details way. I am looking to find a way to optimize the geometry of<br>
peptides with different sizes. I don't have a supercomputer so I need a=
<br>
simple, rather accurate way to do it (i know this is the dream of having<br=
>
such software, I mean with a good accuracy) however, the speed is very<br>
important for me because with hyperchem it takes like forever.<br>
<br>
So, I need a way to find the best conformer of a peptide and then optimize<=
br>
it geometry.<br>
<br>
Any suggestion is welcome<br>
Best Regards,<br>
Mohammad<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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</blockquote></div><br><br>-- <br><div dir=3D"ltr"><div>John McKelvey<br>54=
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iv></div><br>
--047d7b2e148d074e5b051e37d836--
From owner-chemistry@ccl.net Wed Aug 26 16:42:01 2015
From: "Hadi Dinpajooh mdinpajo : asu.edu" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL:G: Excited States: Transition Dipole Moments
Message-Id: <-51622-150826154142-16139-fwbd616JxCCIVBSj8pwLhQ[A]server.ccl.net>
X-Original-From: Hadi Dinpajooh <mdinpajo:+:asu.edu>
Content-Type: multipart/alternative; boundary=089e0122aefae874c2051e3c0959
Date: Wed, 26 Aug 2015 12:41:17 -0700
MIME-Version: 1.0
Sent to CCL by: Hadi Dinpajooh [mdinpajo_-_asu.edu]
--089e0122aefae874c2051e3c0959
Content-Type: text/plain; charset=UTF-8
Hi,
I use Zindo or CIS or TD to obtain all transition dipole moments, i.e.
ground to excited states and excited to excited states. I used
AllTransitionDensities Keyword in Gaussian09: #P Zindo(NStates
50,AllTransitionDensities)
SCF=QC
I noticed that in the gaussian output file, all transition dipole moments
> from the ground state to excited states are reported. Also, the
off-diagonal terms of the transition dipole moments from excited to excited
states are reported. Interestingly, I have not yet found the diagonal terms
of the transition dipole moments from the excited to excited states. I was
hoping IOp (IOp(6/22), etc.) would help but I have not yet found the
solution to get the 50 diagonal transition dipole moment terms. Any
suggestions about what to try next?
Thanks,
Hadi
Mohammadhasan Dinpajooh
Arizona State University
--089e0122aefae874c2051e3c0959
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable
<div dir=3D"ltr"><div style=3D"font-size:12.8000001907349px">Hi,</div><div =
style=3D"font-size:12.8000001907349px"><br></div><div style=3D"font-size:12=
.8000001907349px">I use=C2=A0Zindo=C2=A0or CIS or TD to obtain all transiti=
on dipole moments, i.e. ground to excited states and excited to excited sta=
tes. I used AllTransitionDensities Keyword in Gaussian09:=C2=A0<span style=
=3D"font-size:12.8000001907349px">#P=C2=A0</span>Zindo<span style=3D"font-s=
ize:12.8000001907349px">(NStates 50,</span><span style=3D"font-size:12.8000=
001907349px">AllTransitionDensities) SCF=3DQC</span></div><div style=3D"fon=
t-size:12.8000001907349px"><br></div><div style=3D"font-size:12.80000019073=
49px">I noticed that in the gaussian output file, all transition dipole mom=
ents from the ground state to excited states are reported. Also, the off-di=
agonal terms of the transition dipole moments from=C2=A0excited to excited =
states are reported. Interestingly, I have not yet found the diagonal terms=
of the transition dipole moments from the excited to excited states. I was=
hoping IOp (IOp(6/22), etc.) would=C2=A0help=C2=A0but I have not yet found=
the solution to get the 50 diagonal transition dipole moment terms. Any su=
ggestions about what to try next? =C2=A0 =C2=A0=C2=A0</div><div style=3D"fo=
nt-size:12.8000001907349px"><br></div><div style=3D"font-size:12.8000001907=
349px">Thanks,</div><div style=3D"font-size:12.8000001907349px">Hadi</div><=
div style=3D"font-size:12.8000001907349px"><br></div><div style=3D"font-siz=
e:12.8000001907349px">Mohammadhasan Dinpajooh</div><div style=3D"font-size:=
12.8000001907349px">Arizona State University</div></div>
--089e0122aefae874c2051e3c0959--
From owner-chemistry@ccl.net Wed Aug 26 19:53:01 2015
From: "Lars Goerigk lars.goerigk%%unimelb.edu.au" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: peptides geometry optimization
Message-Id: <-51623-150826195207-6669-tObad7x9ufgPNy3mD5hV4w+*+server.ccl.net>
X-Original-From: "Lars Goerigk" <lars.goerigk * unimelb.edu.au>
Date: Wed, 26 Aug 2015 19:52:06 -0400
Sent to CCL by: "Lars Goerigk" [lars.goerigk++unimelb.edu.au]
Hi Mohammad,
I agree with John that ORCA would be good a solution for you. It is free for academics and very efficient.
As computing time and resources seem to be the issue, you may need to choose an economically feasible level of theory. In particular, you are probably thinking about using a DFT approximation with a small basis set.
I have a few comments on that:
When treating peptide conformations with a DFT approximation, you will definitely need to include a London-dispersion correction; London dispersion does not only affect relative energies between conformers, but also their structural properties. By choosing a small basis set, you may speed up the calculation, however, you introduce an artificial overstabilisation of intramolecular noncovalent interactions due to the basis-set superposition error (BSSE). For both problems, computationally efficient remedies exist: Grimmes DFT-D3(BJ) dispersion and gCP BSSE corrections. Both corrections are implemented in ORCA.
Besides BSSE, small basis sets also induce other basis-set incompleteness errors, which is why in the end you will have to rely on some error cancellation between your chosen method and basis set.
About two years ago, it was studied which cheap levels of theories were efficient and reasonably accurate for peptide optimisation.
J. Chem. Theory Comput 2013, 9, 3240, http://pubs.acs.org/doi/abs/10.1021/ct400321m
Here is a short summary:
1) If you can afford a triple-zeta basis set, then Truhlars PW6B95 is recommended (with a dispersion correction, but without BSSE correction): PW6B95-D3/(aug-)cc-pVTZ or PW6B95-D3/def2-TZVP.
2) If you have to go down to a double-zeta basis set, then you need a BSSE correction and PW6B95-D3-gCP/6-31G(d) or PW6B95-D3-gCP/SVP were recommended.
3) It turned out that dispersion- and BSSE-corrected Hartree-Fock theory also does a very good job with a double-zeta basis set without polarisation functions: HF-D3-gCP/SV. The only exception was to use SVP instead of SV for sulfur atoms.
The finding that HF-D3-gCP/SV is a good alternative to DFT approximations was later confirmed for an optimisation of a large protein fragment. In fact, HF caused less convergence and other technical problems than DFT approximations:
J. Phys. Chem. B 2014, 118, 14612, http://pubs.acs.org/doi/abs/10.1021/jp510148h.
Finally, it is also worth to have a look at Grimmes new PBEh-3c method, which also provides very good peptide structures at a very small computational cost:
J. Chem. Phys. 2015, 143, 054107, http://scitation.aip.org/content/aip/journal/jcp/143/5/10.1063/1.4927476.
I hope this helped.
Cheers,
Lars
---
Dr. Lars Goerigk
ARC DECRA Fellow
School of Chemistry
The University of Melbourne
VIC 3010
Australia
Research profile:
http://www.chemistry.unimelb.edu.au/dr-lars-goerigk
List of my publications:
http://www.researcherid.com/rid/D-3717-2009
E-mail: lars.goerigk^^unimelb.edu.au
Follow me on Twitter: https://twitter.com/lgoer_compchem
---------------------------------------------------------------------
On 27 Aug 2015, at 12:41 am, John McKelvey jmmckel||gmail.com <owner-chemistry^^ccl.net> wrote:
Mohammed,
An free code that can be very efficient is ORCA. It runs parallel on both Windows and Linux machines with the appropriate hardware. It also can run efficiently on a single core machine. It can handle many types of basis sets, with many being built in.
Hope this helps.
John
On Wednesday, August 26, 2015, Mohammad Goodarzi mohammad.godarzi()gmail.com <owner-chemistry,+,ccl.net> wrote:
Sent to CCL by: "Mohammad Goodarzi" [mohammad.godarzi++gmail.com]
Hello,
I have a general question and I would like to know your thought in a
details way. I am looking to find a way to optimize the geometry of
peptides with different sizes. I don't have a supercomputer so I need a
simple, rather accurate way to do it (i know this is the dream of having
such software, I mean with a good accuracy) however, the speed is very
important for me because with hyperchem it takes like forever.
So, I need a way to find the best conformer of a peptide and then optimize
it geometry.
Any suggestion is welcome
Best Regards,
MohammadE-mail to subscribers: CHEMISTRY,+,ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST,+,ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt