From owner-chemistry@ccl.net Wed Feb 4 00:26:00 2009 From: "Isabelle Navizet navizet-.-univ-mlv.fr" To: CCL Subject: CCL:G: the charge problem in ONIOM method in Gaussian Message-Id: <-38549-090204001639-16420-qY0HNHHi3ag+/7wZA+t/+w*o*server.ccl.net> X-Original-From: Isabelle Navizet Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 04 Feb 2009 13:21:03 +0800 Mime-Version: 1.0 Sent to CCL by: Isabelle Navizet [navizet:univ-mlv.fr] Hello Zhong Jie Liang, It is not normal that your real system (the sum of all atoms) does not have integer charge !!! What do you use as low level ? Amber ? In this case this means that there are wrong charges in your input file. Gaussview is not able to put the right charges in all cases for amber. You should check by hand that the software did not put some zeros in place of charges. Isabelle On Tue, 2009-02-03 at 20:53 -0500, Zhong jie Liang zjliang]^[mail.shcnc.ac.cn wrote: > Sent to CCL by: "Zhong jie Liang" [zjliang..mail.shcnc.ac.cn] > Dear Jean-Christophe, > Thanks for your answer very much.But I still have the problem . > That is how to get the net charge. I know it is easy to get the net charge with Sybyl software. But the charge Sybyl uses is diffenrent from the charge used in GaussianView software, especially that Sybyl adds different charge types on the protein residues and ligands,which affects the result.I don't know if GaussianView can get the net charge on the whole molecule easily.This is not a big problem,but I want to make it clearly. > Wish your answer.Thanks. > -- ------------------------------------------------------------------------ Isabelle Navizet ä¼ŠèŽŽ add 1: Beijing Normal University, Department of Chemistry, room 517 add 2: UniversitÃ© Paris-Est, Laboratoire ModÃ©lisation et Simulation Multi Echelle, MSME FRE3160 CNRS, 5 bd Descartes, 77454 Marne-la-Vallee, France equipe de Chimie Theorique de l'Universite de Marne la Vallee From owner-chemistry@ccl.net Wed Feb 4 02:20:00 2009 From: "Joaquin Barroso Flores joaco_barroso]~[yahoo.com" To: CCL Subject: CCL:G: Problem with an NBO calculation. Message-Id: <-38550-090204021644-3161-VthzCcAUNqu6Iv+2AZKPLQ .. server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Type: multipart/alternative; boundary="0-570650004-1233731790=:77337" Date: Tue, 3 Feb 2009 23:16:30 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso:+:yahoo.com] --0-570650004-1233731790=:77337 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Maybe you should send us more of your input (the deletion section for insta= nce). Anyway, I think its not possible to get a deletion analysis and save = the nbo's at the same time. Try dropping the savenbo keyword, and get them = in a separate calculation. Best wishes ******************************************************************** Joaqu= in Barroso-Flores, Ph. D.=C2=A0=20 Facultatea de Chimie Universitatea Babes-Bolyai Cluj-Napoca, Romania http://joaquinbarroso.com Correo alterno: joaquinbarroso''a''chem.ubbcluj.ro joaquin.barroso''a''gmail.com=20 "Blogastronom=C3=ADa": http://joaquinbarroso.blogspot.com ***************= ***************************************************** --- El mar 3-feb-09, D Joshua Dibble ddibble() uci.edu escribi=C3=B3: De:: D Joshua Dibble ddibble() uci.edu Asunto: CCL:G: Problem with an NBO calculation. A: "Flores, Joaquin Barroso " Fecha: martes, 3 febrero, 2009, 10:01 pm Sent to CCL by: "D Joshua Dibble" [ddibble . uci.edu] Hello, I am unable to complete an NBO calculation, particularly the NBO deletion routing. The header to the input file is as follows: %chk=3Daxial.chk %mem=3D1000MB %NProcShared=3D2 # b3lyp/6-311g(d,p) pop=3D(savenbo,nbodel) geom=3Dconnectivity iop(5/48=3D1= 0000) scf=3Dtight=20 The output is: N-N=3D 1.094452818274D+03 E-N=3D-3.791025927973D+03 KE=3D 6.929502473477D+= 02 NtrOpn-Old failed. Error termination via Lnk1e in /modfac/apps//g03/l607.exe at Tue Feb 3 19:11:22 2009. Job cpu time: 0 days 0 hours 16 minutes 51.1 seconds. File lengths (MBytes): RWF=3D 99 Int=3D 0 D2E=3D 0 Chk=3D = 5 Scr=3D =20 1=20 Running Gaussian 03 E.01, NBO version 3. Does anyone know what this error means? Thank you for your time, D. Joshua Dibble ddibble a uci.edu -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt=0A=0A__________________________________________________=0ACorreo Yahoo!=0A= Espacio para todos tus mensajes, antivirus y antispam =C2=A1gratis! =0AReg= =C3=ADstrate ya - http://correo.yahoo.com.mx/ --0-570650004-1233731790=:77337 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

Maybe you should send us more of your input (= the deletion section for instance). Anyway, I think its not possible to get= a deletion analysis and save the nbo's at the same time. Try dropping the = savenbo keyword, and get them in a separate calculation.

Best wishes=

***********************************************= *********************

Joaquin Barroso-Flores, Ph. = D.

= Facultatea de Chimie
Universitatea Babes-Bolyai
Cluj-Napoca, Romania<= br>
http://joaquinbarroso.com

Correo alterno:
joaquinbarroso''a''chem.ubbcluj.ro

joaquin.barroso''a''gmail.com
"Blogastronom=C3=ADa": ht= tp://joaquinbarroso.blogspot.com

**********= **********************************************************

---= El mar 3-feb-09, D Joshua Dibble ddibble() uci.edu <owner-chemist= ry++ccl.net> escribi=C3=B3:

De:: D Jo= shua Dibble ddibble() uci.edu <owner-chemistry++ccl.net>
Asunto: CC= L:G: Problem with an NBO calculation.
A: "Flores, Joaquin Barroso -id#4b= i-" <joaco_barroso++yahoo.com>
Fecha: martes, 3 febrero, 2009, 10:0= 1 pm

Sent
 to CCL by: "D Joshua Dibble" [ddibble . uci.edu]
Hello,

I am una=
ble to complete an NBO calculation, particularly the NBO deletion
routin=
g.  The header to the input file is as follows:

%chk=3Daxial.chk
=
%mem=3D1000MB
%NProcShared=3D2
# b3lyp/6-311g(d,p) pop=3D(savenbo,nbo=
del) geom=3Dconnectivity iop(5/48=3D10000)
scf=3Dtight 

The outpu=
t is:

N-N=3D 1.094452818274D+03 E-N=3D-3.791025927973D+03  KE=3D 6.9=
29502473477D+02
NtrOpn-Old failed.
Error termination via Lnk1e in /mo=
dfac/apps//g03/l607.exe at Tue Feb  3
19:11:22 2009.
Job cpu time:  0=
 days  0 hours 16 minutes 51.1 seconds.
File lengths (MBytes):  RWF=3D  =
   99 Int=3D      0 D2E=3D      0 Chk=3D      5 Scr=3D   
  1 


Running Gaussian 03 E.01, NBO version 3.

Does anyone know what=
 this error means?

Thank you for your time,
D. Joshua Dibble
d=
dibble a uci.edu



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Reg=C3=ADstrate ya - http://correo.yahoo.com.mx/ --0-570650004-1233731790=:77337-- From owner-chemistry@ccl.net Wed Feb 4 07:59:00 2009 From: "Cristian V. Diaconu cvdiaconu!A!rice.edu" To: CCL Subject: CCL:G: Broken Symmetry Singlet Excited State Message-Id: <-38551-090204015255-706-dSTmc4k7q7/tZkHuJp78Ew.:.server.ccl.net> X-Original-From: "Cristian V. Diaconu" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 04 Feb 2009 00:15:32 -0600 MIME-Version: 1.0 Sent to CCL by: "Cristian V. Diaconu" [cvdiaconu~!~rice.edu] Hello Sue, The total energy reported by Gaussian is not for 'annihilated' wave function, but for the single determinant that it uses in the Kohn-Sham scheme (for DFT there isn't really any wave function). There are ways to extract the energy of the pure singlet from the broken symmetry state, but for DFT they only work in certain cases. Please look at discussions in: J. Chem. Phys. 121, 10026 (2004) J. Chem. Phys. 74, 5737 (1981) Coord. Chem. Rev. 238–239, 187 (2003) C. J. Cramer, in Essentials of Computational Chemistry. Theories and Models. (Wiley, Chichester, 2002), Chap. 14.4, pp. 456 – 459. For example, for a molecule with two unpaired electrons on two sites which interact weakly (e.g., H2 molecule stretched, with a large bond length, say 10 Angstroms), if ~ 1, E(singlet) = 2 E(broken sym) - E(triplet) I hope this helps. If you have further questions, please include a little detail on the system you are looking at. Best regards, Chris Sue L chsue2004(~)yahoo.com wrote: > Sent to CCL by: "Sue L" [chsue2004..yahoo.com] > Hi, > > I am running a DFT open-shell singlet calculation using Gaussian 03 to obtain a broken symmetry singlet excited state. Does anyone know whether the electronic energy calculated at the end based on the annihilated wave function or not? > > Thank you very much! > > Best regards, > Sue> > > > -- Cristian V. Diaconu Postdoctoral Research Associate Department of Chemistry - MS60 Rice University PO Box 1892 Houston, TX 77251-1892 Phone: 713-348-3734 Email: cvdiaconu:-:rice.edu From owner-chemistry@ccl.net Wed Feb 4 10:07:01 2009 From: "Jean-Christophe Poully poully%%galilee.univ-paris13.fr" To: CCL Subject: CCL:G: the charge problem in ONIOM method in Gaussian Message-Id: <-38552-090204100547-1875-Q/A/JbvyybFHtaAGmt45jg ~ server.ccl.net> X-Original-From: Jean-Christophe Poully Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Wed, 04 Feb 2009 16:05:24 +0100 Mime-Version: 1.0 Sent to CCL by: Jean-Christophe Poully [poully[a]galilee.univ-paris13.fr] Dear Zhong jie, You cannot compute the net charge and partial=20 charges of your system with Gaussview, but you=20 can do it with Chimera, which is free for=20 academics=20 http://www.cgl.ucsf.edu/chimera/download.html If=20 you work with proteins and ligands, then I guess=20 you only have protonated or deprotonated species,=20 so if the net charge is still not an integer, and=20 if your system is not too big, then you should=20 directly look for the protonation and=20 deprotonation sites with Gaussview to know the=20 net charge and put it in the Gaussian .gjf file. Hope it helps! JC Poully At 02:53 04/02/2009, you wrote: >Sent to CCL by: "Zhong jie Liang" [zjliang..mail.shcnc.ac.cn] >Dear Jean-Christophe, > Thanks for your answer very much.But I still have the problem . > That is how to get the net charge. I know it=20 > is easy to get the net charge with Sybyl=20 > software. But the charge Sybyl uses is=20 > diffenrent from the charge used in GaussianView=20 > software, especially that Sybyl adds different=20 > charge types on the protein residues and=20 > ligands,which affects the result.I don't know=20 > if GaussianView can get the net charge on the=20 > whole molecule easily.This is not a big problem,but I want to make it= clearly. >Wish your answer.Thanks. > > > > > > > > > > > ZhongjieLiang > zjliang() mail.shcnc.ac.cn > Shanghai Institute of Materia Medica > > > >-=3D This is automatically added to each message by the mailing script =3D-Jean-Christophe Poully Doctorant dans l'=E9quipe AMIBES Laboratoire de Physique des Lasers Institut Galil=E9e 99, avenue JB Cl=E9ment 93430 VILLETANEUSE Bureau B002 0149403853=20 From owner-chemistry@ccl.net Wed Feb 4 16:41:00 2009 From: "David A. Mannock dmannock++ualberta.ca" To: CCL Subject: CCL: Target identification for reported inhibitor Message-Id: <-38553-090203144847-14863-5uyWPV54/ggZpcqh5V1YNA%%server.ccl.net> X-Original-From: "David A. Mannock" Content-Type: multipart/alternative; boundary="=====================_1760032390==.ALT" Date: Tue, 03 Feb 2009 12:14:16 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Mannock" [dmannock%%ualberta.ca] --=====================_1760032390==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed A target or the target? Sounds like you need a biochemist and the willingness to do some experiments! Please excuse the use of the dirty word here! David At 04:26 AM 03/02/2009, you wrote: >Hi All; >I have a molecule in my hand which is well reported antitubercular >drug but the respective target protein is not known! Can anyone >suggest me how can i find the target for this ligand? > --=====================_1760032390==.ALT Content-Type: text/html; charset="us-ascii" A target or the target? Sounds like you need a biochemist and the willingness to do some experiments! Please excuse the use of the dirty word here! David

At 04:26 AM 03/02/2009, you wrote:

Hi All;
I have a molecule in my hand which is well reported antitubercular drug but the respective target protein is not known! Can anyone suggest me how can i find the target for this ligand?

--=====================_1760032390==.ALT-- From owner-chemistry@ccl.net Wed Feb 4 20:55:00 2009 From: "Zhong jie Liang zjliang_+_mail.shcnc.ac.cn" To: CCL Subject: CCL: how to deal with the result of the ONIOM method Message-Id: <-38554-090204205258-7881-7Z8Unu67elR0eX/wrmpP6w-x-server.ccl.net> X-Original-From: "Zhong jie Liang" Date: Wed, 4 Feb 2009 20:52:54 -0500 Sent to CCL by: "Zhong jie Liang" [zjliang#,#mail.shcnc.ac.cn] Thanks for Jean-Christophe and Isabelle's help. I have known my charge problem and solved it. Now I am doing the first optimization. The next is to do the scan.I don't know how to deal with the result completely. What I need to do is to get the energy of every step and then make an adiabatic potential energy surface as a function of two different distances. Is that right? Hope to get answer very much. Thanks. ZhongjieLiang zjliang:mail.shcnc.ac.cn Shanghai Institute of Materia Medica From owner-chemistry@ccl.net Wed Feb 4 23:51:02 2009 From: "Sue Lam chsue2004#,#yahoo.com" To: CCL Subject: CCL:G: Broken Symmetry Singlet Excited State Message-Id: <-38555-090204224142-10972-7LRjA6x37X9Brs2cSjYLPg**server.ccl.net> X-Original-From: Sue Lam Content-Type: multipart/alternative; boundary="0-712308165-1233801683=:21903" Date: Wed, 4 Feb 2009 18:41:23 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004**yahoo.com] --0-712308165-1233801683=:21903 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hello Chris, =A0 Thank you very much for your reply. I am studying a reaction, in which the = transition state=A0contain biradical character. I=A0have tired=A0to extract= the energy of the pure singlet from the broken symmetry state by using the= spin-correction procedure which was proposed by Yamaguchi et al (Chem. Phy= s. Lett. 1994, 231, 25=9633) =A0 E(singlet) =3D E(broken symmetry from UDFT) + fSC[E(broken symmetry from UD= FT =96 E(triplet from UDFT)) =A0 Where fSC =3D 1 / [3 - 1] =A0 S^2: expectation value of the total spin =A0 The S^2 before and after the annihilation are listed in the Gaussian output= . In my case,=20 =A0 Annihilation of the first spin contaminant: S^2 before annihilation=A0=A0=A0=A0 0.8631,=A0=A0 after=A0=A0=A0=A0 0.4136 =A0 I am not sure that whether I should use the S^2 before or after the annihil= ation for the projection method.=20 =A0 Best regards, Sue --- On Wed, 2/4/09, Cristian V. Diaconu cvdiaconu!A!rice.edu wrote: > From: Cristian V. Diaconu cvdiaconu!A!rice.edu Subject: CCL:G: Broken Symmetry Singlet Excited State To: "L, Sue " Date: Wednesday, February 4, 2009, 2:15 PM Sent to CCL by: "Cristian V. Diaconu" [cvdiaconu~!~rice.edu] Hello Sue, The total energy reported by Gaussian is not for 'annihilated' wave function, but for the single determinant that it uses in the Kohn-Sham sche= me (for DFT there isn't really any wave function). There are ways to extract the energy of the pure singlet from the broken symmetry state, but for DFT = they only work in certain cases. Please look at discussions in: J. Chem. Phys. 121, 10026 (2004) J. Chem. Phys. 74, 5737 (1981) Coord. Chem. Rev. 238=96239, 187 (2003) C. J. Cramer, in Essentials of Computational Chemistry. Theories and Models= . (Wiley, Chichester, 2002), Chap. 14.4, pp. 456 =96 459. For example, for a molecule with two unpaired electrons on two sites which interact weakly (e.g., H2 molecule stretched, with a large bond length, say= 10 Angstroms), if ~ 1, E(singlet) =3D 2 E(broken sym) - E(triplet) I hope this helps. If you have further questions, please include a little detail on the system you are looking at. Best regards, Chris Sue L chsue2004(~)yahoo.com wrote: > Sent to CCL by: "Sue L" [chsue2004..yahoo.com] > Hi,=20 > I am running a DFT open-shell singlet calculation using Gaussian 03 to obtain a broken symmetry singlet excited state. Does anyone know whether th= e electronic energy calculated at the end based on the annihilated wave funct= ion or not?=20 > Thank you very much! >=20 > Best regards, > Sue>=20 >=20 >=20 -- Cristian V. Diaconu Postdoctoral Research Associate Department of Chemistry - MS60 Rice University PO Box 1892 Houston, TX 77251-1892 Phone: 713-348-3734 Email: cvdiaconu-x-rice.edu -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt=0A=0A=0A --0-712308165-1233801683=:21903 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable

Hello Chris,

Thank you very much for = your reply. I am studying a reaction, in which the transition state co= ntain biradical character. I have tired to extract the energy of = the pure singlet from the broken symmetry state by using the spin-correctio= n procedure which was proposed by Yamaguchi et al (Chem. Phys. Lett. 1994, 231, 25=9633)

E(singlet) =3D E(broken symmet= ry from UDFT) + fSC[E(broken symmetry from UDFT =96 E(triplet from UDFT))

Where fSC =3D 1<S^2> / [= 3<S^2> - 1<S^2>]

S^2: expectation value of the = total spin

The S^2 before and after the a= nnihilation are listed in the Gaussian output. In my case,

Annihilation of the firs= t spin contaminant:

S^2 before annihilation 0.8631, after 0.4136

I am not sure that whether I s= hould use the S^2 before or after the annihilation for the projection metho= d.

Best regards,

Sue

--- On= Wed, 2/4/09, Cristian V. Diaconu cvdiaconu!A!rice.edu <owner-chem= istry]|[ccl.net> wrote:

From: Cristian V. Diaconu cvdiaconu!A!rice.edu <ow= ner-chemistry]|[ccl.net>
Subject: CCL:G: Broken Symmetry Singlet Excite= d State
To: "L, Sue " <chsue2004]|[yahoo.com>
Date: Wedne= sday, February 4, 2009, 2:15 PM

Sent to CCL by: "Cristian V. Di= aconu" [cvdiaconu~!~rice.edu] Hello Sue, The total energy reported by Gaussian is not for 'annihilated' wave function, but for the single determinant that it uses in the Kohn-Sham sche= me (for DFT there isn't really any wave function). There are ways to extract the energy of the pure singlet from the broken symmetry state, but for DFT = they only work in certain cases. Please look at discussions in: J. Chem. Phys. 121, 10026 (2004) J. Chem. Phys. 74, 5737 (1981) Coord. Chem. Rev. 238=96239, 187 (2003) C. J. Cramer, in Essentials of Computational Chemistry. Theories and Models= . (Wiley, Chichester, 2002), Chap. 14.4, pp. 456 =96 459. For example, for a molecule with two unpaired electrons on two sites which interact weakly (e.g., H2 molecule stretched, with a large bond length, say= 10 Angstroms), if <S^2> ~ 1, E(singlet) =3D 2 E(broken sym) - E(triplet) I hope this helps. If you have further questions, please include a little detail on the system you are looking at. Best regards, Chris Sue L chsue2004(~)yahoo.com wrote: > Sent to CCL by: "Sue L" [chsue2004..yahoo.com] > Hi,=20 > I am running a DFT open-shell singlet calculation using Gaussian 03 to obtain a broken symmetry singlet excited state. Does anyone know whether th= e electronic energy calculated at the end based on the annihilated wave funct= ion or not?=20 > Thank you very much! >=20 > Best regards, > Sue>=20 >=20 >=20 -- Cristian V. Diaconu Postdoctoral Research Associate Department of Chemistry - MS60 Rice University PO Box 1892 Houston, TX 77251-1892 Phone: 713-348-3734 Email: cvdiaconu-x-rice.edu -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

=0A=0A --0-712308165-1233801683=:21903--