From owner-chemistry@ccl.net Tue Jun 26 01:00:00 2007 From: "Alejandro Velazquez mesientovivo*hotmail.com" To: CCL Subject: CCL: How can I print polarizabilities (alphas) in ADF? Message-Id: <-34563-070625203912-12421-8UBvoV/Hs7aRqAksO07kdA]|[server.ccl.net> X-Original-From: "Alejandro Velazquez" Date: Mon, 25 Jun 2007 20:39:09 -0400 Sent to CCL by: "Alejandro Velazquez" [mesientovivo]=[hotmail.com] I've been working trying to reproduce polarizabilities and hyperpolarizabilities in ADF package from an article. I have the hyperpolarizabilities (betas), but I haven't found how to modify the input file so the results for polarizabilities (alphas) can be displayed in the output file. Can someone guide me? From owner-chemistry@ccl.net Tue Jun 26 01:35:01 2007 From: "Pedro David Ortiz pedrod-$-fq.uh.cu" To: CCL Subject: CCL: UV-Vis calculations Message-Id: <-34564-070625160527-6370-+NAU8ywlZjXnktzQb7gkzw..server.ccl.net> X-Original-From: "Pedro David Ortiz" Date: Mon, 25 Jun 2007 16:05:22 -0400 Sent to CCL by: "Pedro David Ortiz" [pedrod/./fq.uh.cu] Dear CCL: Im trying to do UV-Vis calculations of C6H5-C6H5 by using DFT TD and CIS. I have obteined very but results with bouth methods: in the range of energy corresponding to experimental absortion there are not signals with significat oscilator strength. All comments about solutions will be very appreciated. Thanks in advance. From owner-chemistry@ccl.net Tue Jun 26 02:12:00 2007 From: "Grace Shen sll513,yahoo.com" To: CCL Subject: CCL: Dock Message-Id: <-34565-070625231104-25262-6lv08iB4xBHOXr6e1xueBw|*|server.ccl.net> X-Original-From: Grace Shen Content-Type: multipart/alternative; boundary="0-1169318750-1182823795=:18004" Date: Mon, 25 Jun 2007 19:09:55 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Grace Shen [sll513 . yahoo.com] --0-1169318750-1182823795=:18004 Content-Type: text/plain; charset=ascii Dear all: I am looking for some references which can give me some instructions or rules on how to do dock manually without using any commercial docking software, such as Glide, Gold, and etc. Your help is highly appreciated! Cheers, Grace ____________________________________________________________________________________ Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 --0-1169318750-1182823795=:18004 Content-Type: text/html; charset=ascii

Dear all:

I am looking for some references which can give me some instructions or rules on how to do dock manually without using any commercial docking software, such as Glide, Gold, and etc. Your help is highly appreciated!

Cheers,

Grace

Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. --0-1169318750-1182823795=:18004-- From owner-chemistry@ccl.net Tue Jun 26 04:23:00 2007 From: "Stan van Gisbergen vangisbergen * scm.com" To: CCL Subject: CCL: How can I print polarizabilities (alphas) in ADF? Message-Id: <-34566-070626041345-20917-3FGNnPUlwe5pwOlFssdnsQ+*+server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-5-523958671 Date: Tue, 26 Jun 2007 09:15:05 +0200 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Stan van Gisbergen [vangisbergen*scm.com] --Apple-Mail-5-523958671 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Alejandro, Please have a look at the ADF user's guide and documented example below (polarizability of Au2): http://www.scm.com/Doc/Doc2006.01/ADF/ADFUsersGuide/page125.html http://www.scm.com/Doc/Doc2006.01/ADF/Examples/page39.html Feel free to contact support a scm.com for additional questions. Best regards, Stan van Gisbergen On Jun 26, 2007, at 2:39 AM, Alejandro Velazquez mesientovivo*hotmail.com wrote: > > Sent to CCL by: "Alejandro Velazquez" [mesientovivo]=[hotmail.com] > I've been working trying to reproduce polarizabilities and > hyperpolarizabilities in ADF package from an article. I have the > hyperpolarizabilities (betas), but I haven't found how to modify > the input > file so the results for polarizabilities (alphas) can be displayed > in the > output file. > > Can someone guide me? > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > Dr. S.J.A. van Gisbergen Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen a scm.com http://www.scm.com T: +31-20-5987626 F: +31-20-5987629 --Apple-Mail-5-523958671 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1

Dear = Alejandro,=A0

Please have a look at the = ADF user's guide and documented example below (polarizability of = Au2):

= http://www.scm.com/Doc/Doc2006.01/ADF/ADFUsersGuide/page125.html

h= ttp://www.scm.com/Doc/Doc2006.01/ADF/Examples/page39.html

Feel free to contact = support a scm.com for additional questions.=A0

Best = regards,

Stan van Gisbergen=A0

On Jun = 26, 2007, at 2:39 AM, Alejandro Velazquez mesientovivo*hotmail.com = wrote:

Sent to CCL by: "Alejandro=A0 Velazquez" = [mesientovivo]=3D[hotmail.com]
I've been = working trying to reproduce polarizabilities and=A0
=A0
=A0
file so the results for polarizabilities (alphas) = can be displayed in the=A0
output = file.

Can someone guide me?

-=3D This is automatically added to each message by = the mailing script =3D-
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Dr. S.J.A. van Gisbergen =A0 = =A0 =A0

Scientific Computing & Modelling NV

Theoretical Chemistry, Vrije = Universiteit

De Boelelaan 1083

1081 HV Amsterdam

The Netherlands=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0

vangisbergen a scm.com =A0

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F: +31-20-5987629 =A0 =A0 = =A0

= --Apple-Mail-5-523958671-- From owner-chemistry@ccl.net Tue Jun 26 05:36:01 2007 From: "Igor Avilov avilovi,+,averell.umh.ac.be" To: CCL Subject: CCL:G: G03 optimization convergence limits Message-Id: <-34567-070626045922-7814-K6On1L9veuAbMNKbMh3bNw[A]server.ccl.net> X-Original-From: "Igor Avilov" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7B7CB.AA8FD0CB" Date: Tue, 26 Jun 2007 10:26:15 +0200 MIME-Version: 1.0 Sent to CCL by: "Igor Avilov" [avilovi[#]averell.umh.ac.be] This is a multi-part message in MIME format. ------_=_NextPart_001_01C7B7CB.AA8FD0CB Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear John, =20 Try using Opt(GDIIS), it helps in cases where the potential energy surface is very flat.=20 =20 Best wishes, Igor Avilov. ________________________________ > From: owner-chemistry#ccl.net [mailto:owner-chemistry#ccl.net]=20 Sent: lundi 25 juin 2007 19:35 To: Igor Avilov Subject: CCL: G03 optimization convergence limits Greetings, Often when there are freely rotating methyl groups one can find that the energy and gradients have converged but there is a large displacement because of the freely rotating or librating methyl group, and a lot of cpu time can go into getting the methyl group to settle down. Does anyone know how to set IOP info to allow a way around this problem [where convergence of the torsion angle of the methyl group is not important]?=20 Thanks! John McKelvey ------_=_NextPart_001_01C7B7CB.AA8FD0CB Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear John,

Try using Opt(GDIIS), it helps in cases where = the potential=20 energy surface is very flat.

Best=20 wishes,

Igor=20 Avilov.

From: owner-chemistry#ccl.net=20 [mailto:owner-chemistry#ccl.net]
Sent: lundi 25 juin 2007=20 19:35
To: Igor Avilov
Subject: CCL: G03 optimization = convergence limits

Greetings,

Often when there are freely rotating methyl = groups=20 one can find that the energy and gradients have converged but there is a = large=20 displacement because of the freely rotating or librating methyl group, = and a lot=20 of cpu time can go into getting the methyl group to settle down. = Does=20 anyone know how to set IOP info to allow a way around this problem = [where=20 convergence of the torsion angle of the methyl group is not important]?=20

Thanks!

John McKelvey
------_=_NextPart_001_01C7B7CB.AA8FD0CB-- From owner-chemistry@ccl.net Tue Jun 26 07:00:00 2007 From: "Maxim Kholin maxim.kholin^^^q-pharm.com" To: CCL Subject: CCL: Dock Message-Id: <-34568-070626033241-16407-uW/xQ0noPpIXXjXpDupVCA],[server.ccl.net> X-Original-From: "Maxim Kholin" Content-Type: multipart/alternative; boundary="----=_NextPart_000_2579_01C7B7E5.A1A7F000" Date: Tue, 26 Jun 2007 11:32:09 +0400 MIME-Version: 1.0 Sent to CCL by: "Maxim Kholin" [maxim.kholin#%#q-pharm.com] This is a multi-part message in MIME format. ------=_NextPart_000_2579_01C7B7E5.A1A7F000 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, You can use now free 1 month trial version of Quantum docking that can = be downloaded at www.q-pharm.com unlike scoring function based approaches as you mentioned it is pure = physics based that gives more accuracy. Max ----- Original Message -----=20 From: Grace Shen sll513,yahoo.com=20 To: Kholin, Maxim N =20 Sent: Tuesday, June 26, 2007 6:09 AM Subject: CCL: Dock Dear all: I am looking for some references which can give me some instructions = or rules on how to do dock manually without using any commercial docking = software, such as Glide, Gold, and etc. Your help is highly appreciated! Cheers, Grace -------------------------------------------------------------------------= ----- Ready for the edge of your seat? Check out tonight's top picks on = Yahoo! TV. ------=_NextPart_000_2579_01C7B7E5.A1A7F000 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello,

You can use now free 1 month = trial=20 version of Quantum docking that can be downloaded at www.q-pharm.com

unlike scoring function based = approaches as you=20 mentioned it is pure physics based that gives more = accuracy.

Max

----- Original Message -----

From:=20 Grace=20 Shen sll513,yahoo.com

To: Kholin, Maxim N =

Sent: Tuesday, June 26, 2007 = 6:09=20 AM

Subject: CCL: Dock

Dear all:

I am looking for some references which can give me some = instructions or=20 rules on how to do dock manually without using any commercial docking=20 software, such as Glide, Gold, and etc. Your help is highly = appreciated!

Cheers,

Grace

Ready for the edge of your seat? Check = out=20 tonight's top picks on Yahoo! TV. ------=_NextPart_000_2579_01C7B7E5.A1A7F000-- From owner-chemistry@ccl.net Tue Jun 26 08:52:01 2007 From: "Zeyar Aung azeyar*i2r.a-star.edu.sg" To: CCL Subject: CCL: Dock Message-Id: <-34569-070626075351-13994-070kFbdsCnN5V6NYnQ5SvQ*server.ccl.net> X-Original-From: "Zeyar Aung" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 26 Jun 2007 18:49:15 +0800 MIME-Version: 1.0 Sent to CCL by: "Zeyar Aung" [azeyar ~~ i2r.a-star.edu.sg] Hi, I use Hex 4.5 which is quite easy to use. www.csd.abdn.ac.uk/hex/ Best regards, zeyar ------------------------------------ Zeyar Aung Research Fellow Institute for Infocomm Research Singapore ------------------------------------ ________________________________ > From: Grace Shen sll513,yahoo.com [mailto:owner-chemistry##ccl.net] Sent: Tue 6/26/2007 10:09 AM To: Zeyar Aung Subject: CCL: Dock Dear all: I am looking for some references which can give me some instructions or rules on how to do dock manually without using any commercial docking software, such as Glide, Gold, and etc. Your help is highly appreciated! Cheers, Grace ________________________________ Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. ------------ Institute For Infocomm Research - Disclaimer ------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------------------------------------------------- From owner-chemistry@ccl.net Tue Jun 26 09:39:00 2007 From: "andras.borosy]=[givaudan.com" To: CCL Subject: CCL: Dock Message-Id: <-34570-070626090032-24961-mm/fmo9iTJYmGhwk2EAIww^server.ccl.net> X-Original-From: andras.borosy|*|givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 00432EA6C1257306_=" Date: Tue, 26 Jun 2007 14:13:47 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy-$-givaudan.com This is a multipart message in MIME format. --=_alternative 00432EA6C1257306_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Mr. Kholin, How much slower Quantum docking then scoring function based docking? Regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Maxim Kholin maxim.kholin^^^q-pharm.com" =20 Sent by: owner-chemistry-$-ccl.net 26/06/2007 09:32 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: Dock Hello, You can use now free 1 month trial version of Quantum docking that can be = downloaded at www.q-pharm.com unlike scoring function based approaches as you mentioned it is pure=20 physics based that gives more accuracy. Max =20 ----- Original Message -----=20 > From: Grace Shen sll513,yahoo.com=20 To: Kholin, Maxim N=20 Sent: Tuesday, June 26, 2007 6:09 AM Subject: CCL: Dock Dear all: =20 I am looking for some references which can give me some instructions or=20 rules on how to do dock manually without using any commercial docking=20 software, such as Glide, Gold, and etc. Your help is highly appreciated! =20 Cheers, =20 Grace Ready for the edge of your seat? Check out tonight's top picks on Yahoo!=20 TV.=20 --=_alternative 00432EA6C1257306_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Mr. Kholin,

How much slower Quantum docking then scoring function bas= ed docking?

Regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf - Switzerland
T:+41-44-824 2164 - F:+41-44-8242926 - http:= //www.givaudan.com

"Maxim Kholin ma= xim.kholin^^^q-pharm.com" <owner-chemistry-$-ccl.net>
Sent by: owner-chemistry-$-ccl.net

26/06/2007 09:32

Please respond to
"CCL Subscribers" <chemistry-$-ccl.net>

To	"Borosy, Andras " <andras.borosy-$-givaudan.com>
cc
Subject	CCL: Dock

Hello,
You can use now free 1 month trial version of Quantum docking that can be downloaded at www.q-ph= arm.com
unlike scoring function based approaches as you mentioned it is pure physics based that gives more accuracy.
Max

----- Original Message -----
From: Grace Shen sll513,yahoo.com
To: Kholin, Maxim N
Sent: Tuesday, June 26, 2007 6:09 AM
Subject: CCL: Dock

Dear all:

I am looking for some references which can give me some instructions or rules on how to do dock manually without using any commerci= al docking software, such as Glide, Gold, and etc. Your help is highly appreci= ated!

Cheers,

Grace

Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV.

--=_alternative 00432EA6C1257306_=-- From owner-chemistry@ccl.net Tue Jun 26 10:14:01 2007 From: "Uwe Huniar uwe.huniar#cosmologic.de" To: CCL Subject: CCL:G: ri-dft (bp86/def-SVP) calculations for Mn(V) oxo porphyrin dimer Message-Id: <-34571-070626094133-13624-MpDYpB807YZMTSyx56nJ+g+*+server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 26 Jun 2007 14:46:28 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar . cosmologic.de] Hello, the SCF convergence in Turbomole can be controlled by: 1. the maximum number of SCF iterations ($scfiterlimit) 2. using a higher DIIS damping ($scfdamp), I would recommend to start with a damping factor between 4 to 8. If that does not help, try: 2.a) set the damping factor to a high value like 15, and limit the number of SCF iterations to, say, 20. 2.b) after that, reduce the damping factor to something like 4 and continue with $scfiterlimit of 300 (or so). You can check the convergence graphically (if gnuplot is installed) by calling cgnce and if the energy starts to oscillate, the damping factor is too high... 3. using another orbital shift ($scforbitalshift) All other procedures might alter your occupation, and that is something you do not want to have in your case. There is a short chapter (6.9) about SCF convergence also in the Tutorial of TURBOMOLE, which can be found in the DOC directory of your Turbomole installation. A detailed description of the keywords can be found in the documentation. Yours, Uwe > I am doing some ri-dft (bp86/def-SVP) calculations for Mn(V) oxo porphyrin > dimer system(s) with TURBOMOLE 5.9.0 > > I managed to optimize the ferromagnatically (F) coupled nonet spin state (F > copled quintets of the individual Mn sites) for the above system. Then I > tried to optimize the anti-ferromagnatically coupled singlet (AF copled > quintets of the individual Mn sites) using the orbitals, geometry of the F > coupled nonet and assigning the exact electron occupancy. But SCF convergence > for the AF singlet was not succeeded. After that, I followed the same > procedure with dft (b3-lyp/def-SVP), but it did not work. > > According to my previous calculations with GAUSSIAN 03 for the same > system(s), AF coupled electronic configurations are quite important than F > coupled spin states. But G03 calculations are time consuming. If I would > manage to optimize the AF coupled spin states using ri-dft, I can save my > time. > > Any comments would be appreciated. > > > W. M. C. Sameera (PhD student) From owner-chemistry@ccl.net Tue Jun 26 11:00:01 2007 From: "errol lewars elewars%a%trentu.ca" To: CCL Subject: CCL: UV-Vis calculations Message-Id: <-34572-070626103104-14718-x5iIhITaPHWx/apxg83acA|*|server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 26 Jun 2007 09:36:46 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars:trentu.ca] 2007 June 26 I don't know what your results for biphenyl look like, but TDDFT or CIS calculations could easilily be out by 20 nm or so, and signals of zero oscillator strength actually show up in the experimental UV as weak absorptions, because of vibrational distortions from perfect symmetry. To get a feel for this do some calculations on small molecules and compare the calculated and exp UVs. The "solution" to your problem is to be allow for the errors in the calculations. E. Lewars === Pedro David Ortiz pedrod-$-fq.uh.cu wrote: >Sent to CCL by: "Pedro David Ortiz" [pedrod/./fq.uh.cu] >Dear CCL: > >Im trying to do UV-Vis calculations of C6H5-C6H5 by using DFT TD and CIS. I have obteined very but results with bouth methods: in the range of energy corresponding to experimental absortion there are not signals with significat oscilator strength. All comments about solutions will be very appreciated. > >Thanks in advance.> > > > > From owner-chemistry@ccl.net Tue Jun 26 11:35:01 2007 From: "Reynier Suardiaz reynier.suardiaz,gmail.com" To: CCL Subject: CCL: S coefficients for EPR-III basis set Message-Id: <-34573-070626112631-14860-JPYcouHcfoDsO0iPV6jDKg**server.ccl.net> X-Original-From: "Reynier Suardiaz" Date: Tue, 26 Jun 2007 11:26:28 -0400 Sent to CCL by: "Reynier Suardiaz" [reynier.suardiaz(!)gmail.com] Dear CCl I need S contraction coefficients for EPR-III basis set. thanks in advance reynier From owner-chemistry@ccl.net Tue Jun 26 13:56:01 2007 From: "Rodney E Versace herrklug_gott^yahoo.com" To: CCL Subject: CCL: Lysine Acetylation Message-Id: <-34574-070626111905-10012-HygKmlyGBw6FoQNriwRIQQ]|[server.ccl.net> X-Original-From: "Rodney E Versace" Date: Tue, 26 Jun 2007 11:19:01 -0400 Sent to CCL by: "Rodney E Versace" [herrklug_gott-,-yahoo.com] Could anybody tell me how can I acetylate a lysine in the pdb, using amber9.0, please? From owner-chemistry@ccl.net Tue Jun 26 14:31:00 2007 From: "Rodney E Versace herrklug_gott-x-yahoo.com" To: CCL Subject: CCL: Lysine Acetylation Message-Id: <-34575-070626110642-3131-d98M/p0pquyq0WUkaSNeeA[a]server.ccl.net> X-Original-From: "Rodney E Versace" Date: Tue, 26 Jun 2007 11:06:39 -0400 Sent to CCL by: "Rodney E Versace" [herrklug_gott]_[yahoo.com] Could anybody tell me how can I acetylate a lysine in the pdb, using amber9.0, please? From owner-chemistry@ccl.net Tue Jun 26 15:06:00 2007 From: "Matthieu Montes matthieu.montes,+,univ-paris5.fr" To: CCL Subject: CCL: Dock Message-Id: <-34576-070626061512-8444-iOp7WLDunAWG1bU8y4Dvig^-^server.ccl.net> X-Original-From: Matthieu Montes Content-Type: multipart/alternative; boundary=Apple-Mail-1-531156896 Date: Tue, 26 Jun 2007 11:15:03 +0200 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Matthieu Montes [matthieu.montes|-|univ-paris5.fr] --Apple-Mail-1-531156896 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Hi Grace, There is this paper from our group which can maybe lend you some help: http://pubs3.acs.org/acs/journals/doilookup?in_doi=3D10.1021/jm050262h it's about a hierarchical VLS protocol combining docking tools =20 accessible for free to academic researchers Regards, Matthieu Montes, --- Matthieu Montes PhD student in molecular modeling Laboratoire de pharmacochimie mol=E9culaire et cellulaire INSERM U648 - University Paris 5 45 rue des Saints P=E8res 75006 Paris Tel : 0142862083 mailto:matthieu.montes()univ-paris5.fr --Apple-Mail-1-531156896 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Hi Grace,

There is this paper from = our group which can maybe lend you some help:

http://pubs3.acs.org/acs/journals/doilookup?in_doi=3D10.1021/jm05026= 2h

it's = about a hierarchical VLS protocol combining docking tools accessible for = free to academic researchers

Regards,

Matthieu = Montes,

---

Matthieu Montes

PhD student in molecular = modeling

Laboratoire de pharmacochimie mol=E9culaire et = cellulaire

INSERM = U648 - University Paris 5

45 rue des Saints P=E8res 75006 Paris

Tel : = 0142862083

mailto:matthieu.montes()univ= -paris5.fr

= --Apple-Mail-1-531156896-- From owner-chemistry@ccl.net Tue Jun 26 15:41:00 2007 From: "Aleksandra N Rudnitskaya Aleksandra.rudnit001]![umb.edu" To: CCL Subject: CCL: strange optimization Message-Id: <-34577-070626100528-27066-tzrnmJSEzRnRMJhx/8BwIA(a)server.ccl.net> X-Original-From: "Aleksandra N Rudnitskaya" Date: Tue, 26 Jun 2007 10:05:24 -0400 Sent to CCL by: "Aleksandra N Rudnitskaya" [Aleksandra.rudnit001%umb.edu] Dear all: I faced with the problem while I optimized radicals, and molecules they appeared first as optimized structures then the program calculated thermochemistry and then right before the answer block it says structure is optimized partly. I tried to reoptimized the structure but it did not work. Item Value Threshold Converged? Maximum Force 0.000277 0.000450 YES RMS Force 0.000084 0.000300 YES Maximum Displacement 0.000898 0.001800 YES RMS Displacement 0.000457 0.001200 YES Predicted change in Energy=-2.303047D-07 Optimization completed. -- Stationary point found. __________________________________________________ .Thermochemistry ___________________________________________________ Item Value Threshold Converged? Maximum Force 0.000277 0.000450 YES RMS Force 0.000084 0.000300 YES Maximum Displacement 0.003152 0.001800 NO RMS Displacement 0.001714 0.001200 NO How should I understand that? Thank you in advance. From owner-chemistry@ccl.net Tue Jun 26 16:15:00 2007 From: "Elaine Meng meng#cgl.ucsf.edu" To: CCL Subject: CCL: new Chimera release Message-Id: <-34578-070626144831-28065-IsH6p8pmmCic0hgdCNXfpw/a\server.ccl.net> X-Original-From: "Elaine Meng" Date: Tue, 26 Jun 2007 14:48:28 -0400 Sent to CCL by: "Elaine Meng" [meng^cgl.ucsf.edu] Hello everyone, A new production release of UCSF Chimera (1.2422) is available from http://www.cgl.ucsf.edu/chimera/download.html Chimera is free for noncommercial use, includes full documentation, and is available for several platforms including Windows, Mac, and Linux. Here are just a few of the changes in the last year or so: - embedded POV-Ray for making glossy, shadowed images; labels included - ability to supersample or raytrace when recording movies - presets for interactive use and publication image scenarios - more input formats: MDL MOL/SDF, CIF/mmCIF, Gromacs trajectories - more Fetch by ID types: EDS (fo-fc) electron density difference map PQS predicted biological unit VIPERdb viral capsid structures - can morph between homologs as well as different conformations - interactive clash/contact detection - partial charge assignment: Amber (Cornell et al.) for standard residues embedded Antechamber to calculate charges for nonstandard residues - sequence alignment viewer allows sequence addition, deletion, reordering - can optimize overlay of density maps - Side View includes "top view" for adjusting stereo params interactively - session files smaller, restore faster - improved preferences handling - updates to handle new atom/res naming conventions in remediated PDB For more details on recent changes, see: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2422.html http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2417.html http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2304.html Best Regards, Elaine ----- Elaine C. Meng, Ph.D. meng^cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Tue Jun 26 16:53:01 2007 From: "Shobe, David David.Shobe[*]sud-chemie.com" To: CCL Subject: CCL:G: strange optimization Message-Id: <-34579-070626163943-12317-SOgVjOkDs8RGyORNg3DR6w.:.server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 26 Jun 2007 22:39:14 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe{=}sud-chemie.com] Aleksandra, During the 'opt' stage of the calculation, an approximate Hessian was used (the Hessian is a matrix of second derivatives which is used to calculate the displacements). A more exact Hessian is calculated in the 'freq' stage, in order to obtain accurate vibrational frequencies and thermochemical parameters. When Gaussian recalculates the displacements using the more exact Hessian, sometimes the displacements are no longer within the convergence criteria. You can use the keywords "opt=readfc geom=check" to reoptimize using the new Hessian. Whether it's worth doing so depends on how large are the displacements, how important an accurate molecular geometry is, and how anal you are. :-) Regards, --David Shobe -----Original Message----- > From: owner-chemistry() ccl.net [mailto:owner-chemistry() ccl.net] Sent: Tuesday, June 26, 2007 10:05 AM To: Shobe, David Subject: CCL: strange optimization Sent to CCL by: "Aleksandra N Rudnitskaya" [Aleksandra.rudnit001%umb.edu] Dear all: I faced with the problem while I optimized radicals, and molecules they appeared first as optimized structures then the program calculated thermochemistry and then right before the answer block it says structure is optimized partly. I tried to reoptimized the structure but it did not work. Item Value Threshold Converged? Maximum Force 0.000277 0.000450 YES RMS Force 0.000084 0.000300 YES Maximum Displacement 0.000898 0.001800 YES RMS Displacement 0.000457 0.001200 YES Predicted change in Energy=-2.303047D-07 Optimization completed. -- Stationary point found. __________________________________________________ .Thermochemistry ___________________________________________________ Item Value Threshold Converged? Maximum Force 0.000277 0.000450 YES RMS Force 0.000084 0.000300 YES Maximum Displacement 0.003152 0.001800 NO RMS Displacement 0.001714 0.001200 NO How should I understand that? Thank you in advance.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Tue Jun 26 17:44:01 2007 From: "Kim Branson kim.branson**gmail.com" To: CCL Subject: CCL: Dock Message-Id: <-34580-070626173956-22821-9I3vCGbzv2/m7ptwUsoXwg[a]server.ccl.net> X-Original-From: Kim Branson Content-Type: multipart/alternative; boundary=Apple-Mail-19-572070257 Date: Tue, 26 Jun 2007 13:36:56 -0700 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Kim Branson [kim.branson a gmail.com] --Apple-Mail-19-572070257 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Autodock 4 is GPL. http://autodock.scripps.edu/ Kim On Jun 26, 2007, at 2:15 AM, Matthieu Montes matthieu.montes,+,univ-=20 paris5.fr wrote: > Hi Grace, > > There is this paper from our group which can maybe lend you some help: > > http://pubs3.acs.org/acs/journals/doilookup?in_doi=3D10.1021/jm050262h > > it's about a hierarchical VLS protocol combining docking tools =20 > accessible for free to academic researchers > > Regards, > > Matthieu Montes, > > > > > --- > > Matthieu Montes > PhD student in molecular modeling > Laboratoire de pharmacochimie mol=E9culaire et cellulaire > INSERM U648 - University Paris 5 > 45 rue des Saints P=E8res 75006 Paris > Tel : 0142862083 > mailto:matthieu.montes*_*univ-paris5.fr > > --Apple-Mail-19-572070257 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1

Autodock 4 is = GPL.=A0

http://autodock.scripps.edu/

Kim

On Jun 26, 2007, = at 2:15 AM, Matthieu Montes matthieu.montes,+,univ-paris5.fr = wrote:

Hi Grace,

There is this paper from = our group which can maybe lend you some help:

http://pubs3.acs.org/acs/journals/doilookup?in_doi=3D10.1021/jm05026= 2h

it's = about a hierarchical VLS protocol combining docking tools accessible for = free to academic researchers

Regards,

Matthieu = Montes,

---

Matthieu = Montes
PhD student in molecular = modeling
Laboratoire de = pharmacochimie mol=E9culaire et cellulaire
INSERM U648 - University Paris 5
45 rue des Saints P=E8res 75006 Paris
Tel : 0142862083
mailto:matthieu.montes*_*= univ-paris5.fr

=

= --Apple-Mail-19-572070257-- From owner-chemistry@ccl.net Tue Jun 26 19:54:00 2007 From: "Grace Shen sll513_._yahoo.com" To: CCL Subject: CCL: looking for free software to generate descriptors Message-Id: <-34581-070626192241-22870-g71OiSMlWdpgOWFkUtiIvA##server.ccl.net> X-Original-From: Grace Shen Content-Type: multipart/alternative; boundary="0-1661154340-1182900154=:9331" Date: Tue, 26 Jun 2007 16:22:34 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Grace Shen [sll513*yahoo.com] --0-1661154340-1182900154=:9331 Content-Type: text/plain; charset=ascii Dear All: Thank you all very much for the help regarding the "DOCK" question previously. Now I am wondering if anyone knows there is any free software which can help me to generate the regular common 1D, 2D and 3D descriptors so that I can perform QSAR analysis efficiently? Thanks, Cheers, Grace Shen ____________________________________________________________________________________ Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/ --0-1661154340-1182900154=:9331 Content-Type: text/html; charset=ascii

Dear All:

Thank you all very much for the help regarding the "DOCK" question previously. Now I am wondering if anyone knows there is any free software which can help me to generate the regular common 1D, 2D and 3D descriptors so that I can perform QSAR analysis efficiently? Thanks,

Cheers,

Grace Shen

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Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out. --0-1661154340-1182900154=:9331-- From owner-chemistry@ccl.net Tue Jun 26 21:36:00 2007 From: "Abdullah Ozkanlar aozkanla^purdue.edu" To: CCL Subject: CCL:G: Gaussian98 Error message when using CEP basis with Polarization Message-Id: <-34582-070626162343-521-zmtyfL830AnpBQ1SEEkRpw]*[server.ccl.net> X-Original-From: "Abdullah Ozkanlar" Date: Tue, 26 Jun 2007 16:23:39 -0400 Sent to CCL by: "Abdullah Ozkanlar" [aozkanla . purdue.edu] Hi, When I run a G98 job using basis set CEP-4G without including polarization function, the job finishes normally. But, whenever I include polarization function ( CEP-4G* ), it gives the following error message : Standard basis: CEP-4G* (6D, 10F) Unable to normalize a contracted basis function. Do you know what it means, and/or how to solve this problem? Thanks. Abdullah Ozkanlar aozkanla-*-purdue.edu