From chemistry-request@ccl.net Thu Dec 2 21:06:05 2004 Received: from web54702.mail.yahoo.com (web54702.mail.yahoo.com [68.142.225.200]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iB3264j5019874 for ; Thu, 2 Dec 2004 21:06:04 -0500 Received: (qmail 89576 invoked by uid 60001); 3 Dec 2004 02:20:58 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=h93YQy86aorTHhO0dIotq78+ryo58nAi3rJBXqRMb8JE7W+hjLdgD8ylC+feT7h9Du3tWx+40WpZVg1rkXXasXv5ZmOSHY727P6ylzouGHCCPgNYqtgGDHMNZXLsYP0sBfZafUXg3Ah7n82eLW0N5qZmmv1uxniuiUQOi8NCD3U= ; Message-ID: <20041203022058.89574.qmail(at)web54702.mail.yahoo.com> Received: from [67.110.18.100] by web54702.mail.yahoo.com via HTTP; Thu, 02 Dec 2004 18:20:58 PST Date: Thu, 2 Dec 2004 18:20:58 -0800 (PST) From: Guosheng Wu Subject: Charge model for simulating protein ligand complex To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=2.5 required=7.5 tests=FROM_ENDS_IN_NUMS, FROM_HAS_ULINE_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello everyone, I guess there seems no consensus so far on what's the best charge model for molecular mechanics. Still one would like to use a consistent and decent (hopefully) model, but the problem I am seeing is that many times people are used to applying different charge models for the simulation of a protein ligand complex. At least I see many papers with such kind of approach. Typically, a quick method such as Gasteiger charge is used for the ligand (small molecule), but more "accurate" charge model (such as CHARMM, AMBER...) is used for protein atoms. However, I am very surprised to see the atomic charges could be very different between Gasteiger model and Quanta templates(CHARMM like charges?), for either protein or ligand. One example shown below is for 1gih (one kinase complex) generated from Quanta program. The signs can even be different: Atom_ID type Gasteiger Quanta_template Quanta_template - Gasteiger 532 HZ2 -0.09 0.35 0.44 520 NZ 0.38 -0.30 -0.68 L_4 C7 0.25 0.59 0.34 L_13 O13 -0.27 -0.56 -0.29 1253 H 0.15 0.25 0.10 1245 N -0.30 -0.40 -0.10 1246 CA 0.10 0.05 -0.05 1247 C 0.23 0.60 0.37 1248 O -0.27 -0.55 -0.28 L_16 N16 -0.25 -0.41 -0.16 L_35 H12 0.06 0.12 0.06 L_15 C15 0.31 0.59 0.28 L_17 O17 -0.25 -0.56 -0.31 [Atom ID for protein or ligand(L_*) ] So it seems true that the results based on such kind of charging approach (protein from an "accurate" model like CHARMM, ligand from quick model like Gasteiger) could be very unrelible. Does anyone have better ideas on this issue? Should we start to blame more on the charge models when we can not get good results? Maybe the best choice is to stick to a single model, (Is Gasteiger charge OK for protein ?), at least the error might be systematically adjusted. -Guosheng __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Fri Dec 3 01:10:52 2004 Received: from prg.traveller.cz (prg.traveller.cz [193.85.2.77]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB36ApkN030962 for ; Fri, 3 Dec 2004 01:10:51 -0500 Received: from Tata (pra-s29140.adsl.dial-up.cz [193.179.29.140]) by prg.traveller.cz (8.13.1/8.13.1/prg) with SMTP id iB36Pf3Q033094 for ; Fri, 3 Dec 2004 07:25:45 +0100 (CET) Message-ID: <001901c4d900$ed8f37b0$6501a8c0@Tata> Reply-To: "Jiri Krechl" From: "Jiri Krechl" To: References: <005401c4d7be$69a38a20$c964a8c0:at:spechem.cz> <41AE6B68.5020002:at:strath.ac.uk> Subject: CCL:smiles to sdf converter Date: Fri, 3 Dec 2004 07:22:51 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1250" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1437 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Many thanks to all who kindly responded to my inquiry for smiles to sdf converter. For interested I would be glad to summarize. Among the manifold suggestions, all of them clever, I found the MolConverter of ChemAxon http://www.chemaxon.com/marvin/doc/user/molconvert.html as best fitting my needs. Thanks Ferenc. Jiri Jiri Krechl t: +420-284 691 500 f: +420-284 690 415 m: +420-602 323 819 e: jiri.krechl:at:spechem.cz --- Outgoing mail was checked virus free Zkontrolovano antivirov}m systimem AVG (http://www.grisoft.cz). Verze: 6.0.804 / Virova baze: 546 - datum vydanm: 30.11. 2004 From chemistry-request@ccl.net Fri Dec 3 04:02:49 2004 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB392nkN007256 for ; Fri, 3 Dec 2004 04:02:49 -0500 Received: from [10.76.212.163] (helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtpsa (TLSv1:RC4-MD5:128) (Exim 4.42) id 1Ca9ZQ-0001ES-9k for CHEMISTRY(at)ccl.net; Fri, 03 Dec 2004 10:17:44 +0100 Message-ID: <41B03028.1050003(at)mpi-bpc.mpg.de> Date: Fri, 03 Dec 2004 10:21:44 +0100 From: Edgar Luttmann User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-DE; rv:1.4) Gecko/20030619 Netscape/7.1 (ax) X-Accept-Language: de-de, de MIME-Version: 1.0 To: CHEMISTRY(at)ccl.net Subject: CCL: DMSO, counter ions and ionization state Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Level: / X-Spam-Report: Content analysis: 0.0 points, 6.0 required X-Virus-Scanned: (clean) by exiscan+sophie X-AUTH-Id: eluttma Dear all, does anyone have experiences with the treatment of charges during peptide MD simulations (with gromacs) in DMSO? The pka of the sidechains as well as the termini might be significantly different in DMSO compared to water and thus I wonder if there is a convenient way to estimate the ionization state of the residues. Furthermore would you just put counter ions into the DMSO - or would you keep the peptide neutral? Any suggestions are welcome and thanks in advance.. Edgar -- ******************************************************* Dr. Edgar Luttmann Max-Planck-Institute for Biophysical Chemistry Department 070 - Theoretical and Computational Biophysics Group Am Fassberg 11, 37077 Goettingen, Germany Tel: +49 551 201-2320, Fax: +49 551 201-2302 E-Mail: edgar.luttmann( at )mpi-bpc.mpg.de / eluttma( at )gwdg.de ******************************************************* From chemistry-request@ccl.net Fri Dec 3 07:36:07 2004 Received: from anubis.medic.chalmers.se (anubis.medic.chalmers.se [129.16.30.218]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB3Ca5iK016153 for ; Fri, 3 Dec 2004 07:36:06 -0500 Received: from fy.chalmers.se (f2-pc31.fy.chalmers.se [129.16.110.231]) by anubis.medic.chalmers.se (Postfix) with ESMTP id 83E5B4072; Fri, 3 Dec 2004 13:50:57 +0100 (CET) Message-ID: <41B06337.7000404^at^fy.chalmers.se> Date: Fri, 03 Dec 2004 13:59:35 +0100 From: Patrik Johansson User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry^at^ccl.net Subject: Cavity volume by electron density? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, Does anyone know how to (crudely) compute the cavity exposd to a guest within e.g. a cryptand by using the electron density of the host? Any free software? /Patrik From chemistry-request@ccl.net Fri Dec 3 12:30:12 2004 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB3HU9iK031598 for ; Fri, 3 Dec 2004 12:30:11 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2655.55) id ; Fri, 3 Dec 2004 15:45:35 -0300 Message-ID: <4DB0991764FED5119A2A000475B057CA1C58C2$at$correio.cetem.gov.br> From: Ian Hovell To: "'chemistry'" Subject: ccl:Using TZ2P basis set in Gaussian Date: Fri, 3 Dec 2004 15:45:34 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C4D968.45C6D020" X-Spam-Status: No, hits=2.0 required=7.5 tests=HTML_FONTCOLOR_UNKNOWN, HTML_MESSAGE,LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C4D968.45C6D020 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, I have been trying without success to use the above triple zeta double polarization basis set with G03w I cannot find any direct reference to this basis set in the manual. =20 Can somebody point me in the right direction please. =20 TIA =20 Ian Hovell - Ph.D.=20 NUCLEO DE MODELAGEM MOLECULAR-NMM=20 Centro de Tecnologia Mineral - CETEM=20 Ministerio da Ci=EAncia e da Tecnologia- MCT=20 Avenida Ip=EA, No 900 - Cidade Universitaria=20 Ilha do Fund=E3o Rio de Janeiro RJ Brasil=20 CEP 21941-590=20 tel 00 55 (xx) 3865 7344 ou 3865 - 7216=20 Fax 00 55 (xx) 22602837 ou 2290-4286=20 e-mail hovell$at$cetem.gov.br =20 ------_=_NextPart_001_01C4D968.45C6D020 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear = CCLers,

I have been trying without success to use the = above triple zeta double polarization basis set with = G03w

I cannot find any direct reference to this = basis set in the manual.

 

=

Can somebody point me in the right direction = please.

 

=

TIA

 

=

<= font color=3Dblack>Ian Hovell - = Ph.D. =

NUCLEO = DE MODELAGEM MOLECULAR-NMM

Centro de Tecnologia Mineral - CETEM

Ministerio da Ci=EAncia e da Tecnologia- MCT

Avenida Ip=EA, No 900 - Cidade Universitaria

Ilha do Fund=E3o Rio de Janeiro RJ Brasil

CEP 21941-590

tel 00 55 (xx) 3865 7344 ou 3865 - 7216

Fax 00 55 (xx) 22602837 ou 2290-4286 <= o:p>

e-mail hovell$at$cetem.gov.br

 =

------_=_NextPart_001_01C4D968.45C6D020-- From chemistry-request@ccl.net Mon Dec 6 02:27:34 2004 Received: from mrbusi2.netcologne.de (mrbusi2.netcologne.de [194.8.194.214]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB67RXGQ009701 for >ccl.net>; Mon, 6 Dec 2004 02:27:34 -0500 Received: from cosmologic.de (xdsl-213-196-255-178.netcologne.de [213.196.255.178]) by mrbusi2.netcologne.de (Postfix) with ESMTP id 33A382401D7; Mon, 6 Dec 2004 08:42:40 +0100 (CET) Message-ID: <41B40D6E.2010203<>cosmologic.de> Date: Mon, 06 Dec 2004 08:42:38 +0100 From: Andreas Klamt >cosmologic.de> User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6b) Gecko/20031205 Thunderbird/0.4 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Edgar Luttmann >mpi-bpc.mpg.de> Cc: CHEMISTRY<>ccl.net Subject: Re: CCL:DMSO, counter ions and ionization state References: <41B03028.1050003<>mpi-bpc.mpg.de> In-Reply-To: <41B03028.1050003<>mpi-bpc.mpg.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=4.4 required=7.5 tests=MY_BAD_DOT,MY_DSL, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Edgar, is it dry (water free) DMSO? Then the only way of deprotonation is producing DMSO-H+ ions and for protonation building DMSO anions. We have proposed a pKa model in DMSO in our paper J. Phys. Chem. A 2003, 107, 9380-9386: "First Principles Calculations of Aqueous pKa Values for Organic and Inorganic Acids Using COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale Andreas Klamt,* Frank Eckert, and Michael Diedenhofen, Michael E. Beck This may outline the way how to do it based on our COSMO-RS method. Andreas Luttmann wrote: > Dear all, > > does anyone have experiences with the treatment of charges during > peptide MD simulations (with gromacs) in DMSO? > > The pka of the sidechains as well as the termini might be > significantly different in DMSO compared to water and thus I wonder if > there is a convenient way to estimate the ionization state of the > residues. Furthermore would you just put counter ions into the DMSO - > or would you keep the peptide neutral? > > Any suggestions are welcome and thanks in advance.. > > Edgar > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt=at=cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@ccl.net Mon Dec 6 02:19:24 2004 Received: from mrbusi2.netcologne.de (mrbusi2.netcologne.de [194.8.194.214]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB67JMGQ009057 for ; Mon, 6 Dec 2004 02:19:22 -0500 Received: from cosmologic.de (xdsl-213-196-221-240.netcologne.de [213.196.221.240]) by mrbusi2.netcologne.de (Postfix) with ESMTP id 89E7B240185; Mon, 6 Dec 2004 08:34:28 +0100 (CET) Message-ID: <41B40B83.4080404(at)cosmologic.de> Date: Mon, 06 Dec 2004 08:34:27 +0100 From: Andreas Klamt User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6b) Gecko/20031205 Thunderbird/0.4 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Patrik Johansson Cc: chemistry(at)ccl.net Subject: Re: CCL:Cavity volume by electron density? References: <41B06337.7000404(at)fy.chalmers.se> In-Reply-To: <41B06337.7000404(at)fy.chalmers.se> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=4.4 required=7.5 tests=MY_BAD_DOT,MY_DSL, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Patrik, I doubt that there is an plausible answer to your question. The right surface is a kind of smoothed van der Waals surface. But there is no proof that this surface is an isodensity surface. Attempts in this direction with solvation models have not been very successful. Andreas Johansson wrote: > Dear CCLers, > > Does anyone know how to (crudely) compute the cavity exposd to a guest > within e.g. a cryptand by using the electron density of the host? Any > free software? > > /Patrik > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY(at)ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST(at)ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow(at)nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt(at)cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@ccl.net Mon Dec 6 06:44:53 2004 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB6BinlO020038 for ; Mon, 6 Dec 2004 06:44:50 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2655.55) id ; Mon, 6 Dec 2004 10:00:31 -0300 Message-ID: <4DB0991764FED5119A2A000475B057CA1C58C3(at)correio.cetem.gov.br> From: Ian Hovell To: "'chemistry'" Subject: CCL:Summary Using TZ2P basis set in Gaussian Date: Mon, 6 Dec 2004 10:00:30 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C4DB93.90D414B0" X-Spam-Status: No, hits=2.0 required=7.5 tests=HTML_FONTCOLOR_UNKNOWN, HTML_MESSAGE,LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C4DB93.90D414B0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable As always A summary to my questions: =20 I have been trying without success to use the above triple zeta double polarization basis set with G03w I cannot find any direct reference to this basis set in the manual. =20 Can somebody point me in the right direction please? =20 The answers I received: =20 =20 Have you looked at the basis set order form? http://www.emsl.pnl.gov/forms/basisform.html =20 Here there is TZ (Dunning) and TZVP. However, the latter says something about DFT orbital. =20 Dear Dr. Hovell, =20 I assume that your questions refers to the triple zeta TZ2P basis set = which N.C. Handy and coworkers have been using in their DFT developments. As = far as I know, it is not implemented in Gaussian. The triple zeta functions are those of Dunning but the polarization functions are more difficult to track. I contacted Prof. Handy last = year and got the following answer: =20 > >Thank you for your enquiry, for the first row it is almost spelt out = in JCP >(108) 2550. It is a Dunning triple zeta and the two sets of d = polarization=20 >exponents are given (they are both for d functions). For Li and H the=20 >polarization functions are p functions. >However the Hydrogen s basis set is different, it is >1 S 3 > 1 52.56 0.025374 > 2 7.903 0.189684 > 3 1.792 0.852933 >2 S 1 > 1 0.502 1.0 >3 S 1 > 1 0.158 1.0 > >it is a scaled version of the Dunning TZ for H. > >For the second row we used 631++G for Na and Al with two sets of d=20 >functions with exponents >Na 0.35, 0.0875 >Al 0.65, 0.1625 >For Si,P,S and Cl we use the 9s6p contraction of the Huzinaga 12s9p = with 3 >sets of d functions which are >Si 1.86, 0.59, 0.20 >P 1.99, 0.63, 0.22 >S 2.12, 0.67, 0.23 >Cl 2.25, 0.71, 0.24 > >Throughout we use 6 cartesian d functions. >We used these basis sets as they are "standard" in CADPAC and in our=20 >experience combine well with DFT.=20 =20 I set up a version of TZ2P for H, C, N, O from the EMSL basis set = library and informations of the publication mentioned (it actually starts a = page 2545). =20 Regards Wolfgang Roth =20 Just A Note: Wolfgang was also very kind enough to send the TZ2P = Gaussian formatted basis set file used by Handy as an attachment. I will be = happy to pass this on to anybody who asks for it. =20 Thanks again for your help =20 Ian Hovell - Ph.D.=20 NUCLEO DE MODELAGEM MOLECULAR-NMM=20 Centro de Tecnologia Mineral - CETEM=20 Ministerio da Ci=EAncia e da Tecnologia- MCT=20 Avenida Ip=EA, No 900 - Cidade Universitaria=20 Ilha do Fund=E3o Rio de Janeiro RJ Brasil=20 CEP 21941-590=20 tel 00 55 (xx) 3865 7344 ou 3865 - 7216=20 Fax 00 55 (xx) 22602837 ou 2290-4286=20 e-mail hovell(at)cetem.gov.br =20 ------_=_NextPart_001_01C4DB93.90D414B0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

As always A summary to my = questions:

 

=

I have been trying without success to use the = above triple zeta double polarization basis set with = G03w

I cannot find any direct reference to this = basis set in the manual.

 

Can somebody point me in the right direction = please?

 

=

The answers I = received:

<= ![if = !supportEmptyParas]> 

=

 

=

Have you looked at the basis set = order form?

http://www.emsl.pnl.gov/forms/basisform.html

=

 

=

Here there is TZ (Dunning) and = TZVP. However, the latter says something

about DFT orbital.

 

=

Dear Dr. = Hovell,

=

 

=

I assume that your questions = refers to the triple zeta TZ2P basis set which

N.C. Handy and coworkers have = been using in their DFT developments. As far

as I know, it is not implemented = in Gaussian.

The triple zeta functions are = those of Dunning but the polarization

functions are more difficult to = track. I contacted Prof. Handy last year

and got the following = answer:

=

 

=

>

=

>Thank you for your enquiry, = for the first row it is almost spelt out in JCP

>(108) 2550. It is a Dunning = triple zeta and the two sets of d polarization

>exponents are given (they = are both for d functions). For Li and H the

>polarization functions are p functions.

>However the Hydrogen s basis = set is different, it is

>1  S  = 3

=

>          = 1      = 52.56    0.025374

=

>          = 2       7.903   = 0.189684

=

>          = 3       1.792   = 0.852933

=

>2  S  = 1

=

>          = 1       0.502   = 1.0

=

>3  S  = 1

=

>          = 1       0.158   = 1.0

=

>

=

>it is a scaled version of = the Dunning TZ for H.

>

=

>For the second row we used = 631++G for Na and Al with two sets of d

>functions with = exponents

=

>Na 0.35, = 0.0875

=

>Al 0.65,  0.1625

>For Si,P,S and Cl we = use  the 9s6p contraction of the = Huzinaga 12s9p with 3

>sets of d functions which = are

=

>Si     1.86, 0.59, = 0.20=

>P      1.99, = 0.63, 0.22

>S      2.12, = 0.67, 0.23

>Cl      2.25, 0.71, = 0.24

=

>

=

>Throughout we use 6 = cartesian d functions.

>We used these basis sets as = they are "standard" in CADPAC and in our

=

>experience combine well with = DFT.

=

 

=

I set up a version of TZ2P for = H, C, N, O from the EMSL basis set library

and informations of the = publication mentioned (it actually starts a page

2545).=

 =

Regards=

Wolfgang Roth

 =

Just A Note: Wolfgang was also = very kind enough to send the TZ2P Gaussian formatted basis set file used by Handy = as an attachment. I will be happy to pass this on to anybody who asks for = it.

=

 

=

Thanks again for your = help

=

 

=

<= font color=3Dblack>Ian Hovell - = Ph.D. =

NUCLEO = DE MODELAGEM MOLECULAR-NMM

Centro de Tecnologia Mineral - CETEM

Ministerio da Ci=EAncia e da Tecnologia- MCT

Avenida Ip=EA, No 900 - Cidade Universitaria

Ilha do Fund=E3o Rio de Janeiro RJ Brasil

CEP 21941-590

tel 00 55 (xx) 3865 7344 ou 3865 - 7216

Fax 00 55 (xx) 22602837 ou 2290-4286 <= o:p>

e-mail hovell(at)cetem.gov.br

 =

------_=_NextPart_001_01C4DB93.90D414B0-- From chemistry-request@ccl.net Mon Dec 6 07:58:49 2004 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB6CwmSe022834 for ; Mon, 6 Dec 2004 07:58:48 -0500 Received: from gollum.unb.ca (gollum.unb.ca [131.202.3.51]) by mailserv.unb.ca (8.13.1/8.13.1) with ESMTP id iB6DDpie014694; Mon, 6 Dec 2004 09:13:51 -0400 Received: from gollum.unb.ca (localhost.localdomain [127.0.0.1]) by gollum.unb.ca (8.12.11/8.12.8) with ESMTP id iB6DDpgp018559; Mon, 6 Dec 2004 09:13:51 -0400 Received: (from apache@localhost) by gollum.unb.ca (8.12.11/8.12.8/Submit) id iB6DDpsr018557; Mon, 6 Dec 2004 09:13:51 -0400 Received: from imac1.chem.unb.ca (imac1.chem.unb.ca [131.202.174.199]) by webmail.unb.ca (IMP) with HTTP for ; Mon, 6 Dec 2004 09:13:51 -0400 Message-ID: <1102338831.41b45b0f68fd5..at..webmail.unb.ca> Date: Mon, 6 Dec 2004 09:13:51 -0400 From: Joe Harriman Reply-to: j.harriman..at..unb.ca To: Guosheng Wu Cc: CCL Subject: Re: CCL:Charge model for simulating protein ligand complex References: <20041203022058.89574.qmail..at..web54702.mail.yahoo.com> In-Reply-To: <20041203022058.89574.qmail..at..web54702.mail.yahoo.com> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.174.199 X-UNB-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: X-MailScanner-From: s808o..at..unb.ca X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Guosheng, We have also looked at the difference between QM based charge methods (namely RESP charges) and alternative methods (AM1-BCC, Gasteiger, etc...). Our tests show that there is quite a difference in the charges between individual atoms using these different methods, this is also seen in your example (atom 532 as an example). We have found the best results using the charges derived from the Amber forcefield for large proteins and QM based RESP charges for ligands. However, depending on the size of your ligands and how many you have this QM based approach may not be suitable. As an alternative to Gasteiger charges you may want to look into AM1-BCC. It is a very fast method and is based on QM calculations. Hope this helps. -Joe Quoting Guosheng Wu : > Hello everyone, > > I guess there seems no consensus so far on what's the best charge model > for molecular mechanics. > > Still one would like to use a consistent and decent (hopefully) model, but > the problem I am seeing is that many times people are used to applying > different charge models for the simulation of a protein ligand complex. > At least I see many papers with such kind of approach. > > Typically, a quick method such as Gasteiger charge is used for the ligand > (small molecule), but more "accurate" charge model (such as CHARMM, > AMBER...) is used for protein atoms. However, I am very surprised to see > the atomic charges could be very different between Gasteiger model and > Quanta templates(CHARMM like charges?), for either protein or ligand. > > One example shown below is for 1gih (one kinase complex) generated from > Quanta program. The signs can even be different: > > Atom_ID type Gasteiger Quanta_template Quanta_template - Gasteiger > 532 HZ2 -0.09 0.35 0.44 > 520 NZ 0.38 -0.30 -0.68 > L_4 C7 0.25 0.59 0.34 > L_13 O13 -0.27 -0.56 -0.29 > 1253 H 0.15 0.25 0.10 > 1245 N -0.30 -0.40 -0.10 > 1246 CA 0.10 0.05 -0.05 > 1247 C 0.23 0.60 0.37 > 1248 O -0.27 -0.55 -0.28 > L_16 N16 -0.25 -0.41 -0.16 > L_35 H12 0.06 0.12 0.06 > L_15 C15 0.31 0.59 0.28 > L_17 O17 -0.25 -0.56 -0.31 > [Atom ID for protein or ligand(L_*) ] > > So it seems true that the results based on such kind of charging approach > (protein from an "accurate" model like CHARMM, ligand from quick model > like Gasteiger) could be very unrelible. > > Does anyone have better ideas on this issue? Should we start to blame > more on the charge models when we can not get good results? Maybe the > best choice is to stick to a single model, (Is Gasteiger charge OK for > protein ?), at least the error might be systematically adjusted. > > -Guosheng > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY..at..ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST..at..ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow..at..nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Mon Dec 6 11:01:02 2004 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB6G11Se006581 for ; Mon, 6 Dec 2004 11:01:01 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.11/jtpda-5.4) with ESMTP id iB6GG1XY049577 for ; Mon, 6 Dec 2004 17:16:01 +0100 (CET) X-Ids: 168 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id iB6GG0Hl398995; Mon, 6 Dec 2004 17:16:00 +0100 (MET) Date: Mon, 6 Dec 2004 17:16:00 +0100 (MET) From: Michel Petitjean Message-Id: <200412061616.iB6GG0Hl398995*at*ds10.itodys.jussieu.fr> To: chemistry*at*ccl.net Subject: CCL: Re: Software for pattern recognition in QSAR studies? X-Greylist: Sender IP whitelisted, not delayed by milter-greylist-1.6rc1 (shiva.jussieu.fr [134.157.0.168]); Mon, 06 Dec 2004 17:16:08 +0100 (CET) X-Miltered: at shiva.jussieu.fr with ID 41B485C1.003 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=0.3 required=7.5 tests=FVGT_s_OBFU_Q1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net To: chemistry*at*ccl.net Subj: CCL: Re: Software for pattern recognition in QSAR studies? > > Renxiao Wang wrote: > > > I am looking for a program that can apply standard pattern recognition > > > techniques. Basically, I want to study a number of samples, each of > > > which can be characterized by some properties. I would like to classify > > > these samples into several groups based on these properties, and then > > > derive a QSAR model for each group. > > >... > > > > When all propoerties are non-numerical (e.g. property 1 takes values > > A or B or C, property 2 takes value red or green or blue, property 3 > > takes values: alpha or beta or gamma or delta, etc...), there is > > a classification method able to compute the optimal partition, > > including the number of classes: very few methods can do this. > > Freeware with reference and documentation: > > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#POP > "E.L. Willighagen" replied: > Classification and Regression Trees (CART) can be do that... there are two or > three packages (one is tree) for R available. See http://cran.r-project.org/. Hiearachical classification methods need to cut the tree. The problem is that cutting the tree is done with the help of arbitrary parameters, these latter being NOT computed from the data only. E.g., in CART, the decision to split a group needs a test, this latter being based most time upon an arbitrary value set by the user. It means that the final number of classes depends on an arbitrary selection of values, done by the user. But even the experienced user cannot be sure to do a suitable selection of parameters. The POP freeware above works without "external" parameters, and compute the number of classes from data only. This dependance of external parameters occurs in many molecular modeling problems, and also occurs in many other fields. Actually, a number of descriptive statisticians work on this problem in the case of numerical variables. It is far from being solved. The solution known for categorical variables is due to F. Marcotorchino in 1981. The scientific community is waiting for an elegant solution in the numerical case. Michel Petitjean, Email: petitjean*at*itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean*at*ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html