From chemistry-request@server.ccl.net Thu Oct 17 03:44:11 2002 Received: from uscmail.usc.es ([193.144.75.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9H7i6f15445 for ; Thu, 17 Oct 2002 03:44:10 -0400 Received: from antonio (priv120.usc.es [193.144.74.118]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id JAA28678 for ; Thu, 17 Oct 2002 09:44:01 +0200 (MET DST) Content-Type: text/plain; charset="iso-8859-1" From: Antonio Fernandez Reply-To: qftramos@usc.es To: chemistry@ccl.net Subject: AM1/PM3 parameters for copper Date: Thu, 17 Oct 2002 09:44:41 -0400 X-Mailer: KMail [version 1.2] MIME-Version: 1.0 Message-Id: <02101709444101.32317@antonio> Content-Transfer-Encoding: 8bit Hi, Does anyone know where could I get the AM1 and/or PM3 parameters for copper? If any, I would like to implement them in MOPAC7.0. Antonio. -- Antonio Fernandez Ramos Dpto de Quimica Fisica Facultade de Quimica Universidade de Santiago de Compostela 15706 Santiago de Compostela Spain E-mail: qftramos@usc.es From chemistry-request@server.ccl.net Thu Oct 17 09:24:58 2002 Received: from aspirine.u-strasbg.fr ([130.79.84.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HDOwf22583 for ; Thu, 17 Oct 2002 09:24:58 -0400 Received: from pharma.u-strasbg.fr (lead2.u-strasbg.fr [130.79.85.21]) (authenticated) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id g9HDOZS26558 for ; Thu, 17 Oct 2002 15:24:35 +0200 Message-ID: <3DAEBA1B.6040203@pharma.u-strasbg.fr> Date: Thu, 17 Oct 2002 15:24:43 +0200 From: Antoine Logean Reply-To: alogean@aspirine.u-strasbg.fr User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: Amber 6 : from amber format to PDB with xleap Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear all, Dear Amber users, My problem is the following : In xleap I prepare the input file for sander : model = loadPDB X.pdb saveAmberParm model X.topol X.xyz quit and I start the minimization with sander : sander -i min.in -o min.out -p X.topol -c X.xyz -r X.minxyz OK all work fine. My question is know by using xleap how can I convert X.minxyz (the sander output in the amber format) in a standart PDB file ? (the equivalent of pdbgen in the previous version) Thank you for your help. Antoine From chemistry-request@server.ccl.net Thu Oct 17 09:47:35 2002 Received: from nikias.cc.uoa.gr ([195.134.68.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HDlYf23068 for ; Thu, 17 Oct 2002 09:47:34 -0400 Received: from localhost (jkerkin@localhost) by nikias.cc.uoa.gr (8.9.3/8.9.3) with SMTP id QAA23941 for ; Thu, 17 Oct 2002 16:47:33 +0300 (EET DST) Date: Thu, 17 Oct 2002 16:47:33 +0300 (EET DST) From: Ioannis Kerkines To: chemistry@ccl.net Subject: Re: CCL:Gamess question In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 16 Oct 2002, Alessandro Contini wrote: > Hi, > Gamess units are Atomic Units o Hartrees, indicated also as AU > 1 AU is equivalent to: > 27.2107 eV > 4.35943E-11 erg > 6.27503E+2 Kcal/mol > 6.57966E+15 Hz > 2.19474E+05 cm-1 > 3.15777E+05 K Using the 1998 CODATA recommended values of the fundamental physical constants (Mohr and Taylor, Rev. Mod. Phys. 72(2), 351 (2000).), these values actually become: 1 a.u. of energy (Hartree) = 27.2113834 eV 627.5094709 kcal/mol 2625.499626 kJ/mol 6.5796839 PHz 219474.631371 cm-1 315774.65 K while 1 a.u. of length (1 bohr) = 0.5291772083 Angstroms. Of course, one has to be careful as to which are the conversion factors within each program. Best regards, Ioannis From chemistry-request@server.ccl.net Thu Oct 17 10:16:54 2002 Received: from sungod.ccs.yorku.ca ([130.63.236.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HEGsf24060 for ; Thu, 17 Oct 2002 10:16:54 -0400 Received: from sunlight.ccs.yorku.ca (sunlight.ccs.yorku.ca [130.63.236.85]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id KAA03838; Thu, 17 Oct 2002 10:16:53 -0400 (EDT) Received: from localhost (serge@localhost) by sunlight.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id KAA08012; Thu, 17 Oct 2002 10:16:52 -0400 (EDT) X-Authentication-Warning: sunlight.ccs.yorku.ca: serge owned process doing -bs Date: Thu, 17 Oct 2002 10:16:51 -0400 (EDT) From: "S.I. Gorelsky" X-X-Sender: serge@sunlight.ccs.yorku.ca To: Antonio Fernandez cc: chemistry@ccl.net Subject: Re: CCL:AM1/PM3 parameters for copper In-Reply-To: <02101709444101.32317@antonio> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Antonio, AM1, PM3, and PM5 parameters for Cu are in MOPAC 2002. However, they are not published yet. With regards, Serge Gorelsky > Hi, > Does anyone know where could I get the AM1 and/or PM3 parameters for copper? > If any, I would like to implement them in MOPAC7.0. > > Antonio. > > -- > Antonio Fernandez Ramos > Dpto de Quimica Fisica > Facultade de Quimica > Universidade de Santiago de Compostela > 15706 Santiago de Compostela > Spain > E-mail: qftramos@usc.es > ________________________________________________________________ S. I. Gorelsky, Ph.D. Department of Chemistry, York University 4700 Keele Street, Toronto, Ontario M3J 1P3 Canada Phone: 416-736-2100 ext#70131 Fax: 416-736-5936 http://www.chem.yorku.ca/grad/SG/ ________________________________________________________________ From chemistry-request@server.ccl.net Thu Oct 17 11:26:36 2002 Received: from dh094-210.csb.sunysb.edu ([129.49.94.210]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HFQaf26672 for ; Thu, 17 Oct 2002 11:26:36 -0400 Received: from localhost (cuigl@localhost) by dh094-210.csb.sunysb.edu (8.11.6/8.11.6) with ESMTP id g9HFKoo24082; Thu, 17 Oct 2002 11:20:50 -0400 X-Authentication-Warning: dh094-210.csb.sunysb.edu: cuigl owned process doing -bs Date: Thu, 17 Oct 2002 11:20:50 -0400 (EDT) From: "CUI, Guanglei" X-X-Sender: cuigl@dh094-210.csb.sunysb.edu To: Antoine Logean cc: chemistry@ccl.net Subject: Re: CCL:Amber 6 : from amber format to PDB with xleap In-Reply-To: <3DAEBA1B.6040203@pharma.u-strasbg.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, To generate PDB file from restrt, you can use, for example, ptraj among many tools available. ptraj $X.topol << EOF trajin X.minxyz trajout X.min.pdb pdb go EOF After ptraj, you can rename X.min.pdb.1 it generates to the name you like. Cheers, On Thu, 17 Oct 2002, Antoine Logean wrote: > Dear all, > Dear Amber users, > > My problem is the following : > > In xleap I prepare the input file for sander : > > model = loadPDB X.pdb > saveAmberParm model X.topol X.xyz > quit > > and I start the minimization with sander : > > sander -i min.in -o min.out -p X.topol -c X.xyz -r X.minxyz > > OK all work fine. My question is know by using xleap how can > I convert X.minxyz (the sander output in the amber format) in > a standart PDB file ? (the equivalent of pdbgen in the previous > version) > > Thank you for your help. > > Antoine > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > -- Guanglei Cui Dept. of Chemistry SUNY at Stony Brook Stony Brook, NY 11790 From chemistry-request@server.ccl.net Thu Oct 17 08:57:17 2002 Received: from srvus010.unitedcatalysts.com ([208.23.162.8]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9HCvHf22054 for ; Thu, 17 Oct 2002 08:57:17 -0400 Received: from 10.1.0.105 by srvus010.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 17 Oct 2002 08:56:08 -0400 Received: by lvlxch02.unitedcatalysts.com with Internet Mail Service (5.5.2653.19) id ; Thu, 17 Oct 2002 08:52:42 -0400 Message-ID: <5CF08BBFE6DE97478C1E76E654CAF908220F5A@lvlxch02.unitedcatalysts.com> From: "Shobe, Dave" To: "'Alessandro Contini'" , "Panagiotis G. Karamertzanis" Cc: CHEMISTRY@ccl.net Subject: RE: Gamess question Date: Thu, 17 Oct 2002 08:52:35 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g9HCvHf22055 Minor clarification: Electrostatic potential is energy per electric charge. All of these energies would be per AU of charge--which is of course the charge of a proton, 1.602176 x 10^-19 Coulomb. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Alessandro Contini [mailto:alessandro.contini@unimi.it] Sent: Wednesday, October 16, 2002 5:06 AM To: Panagiotis G. Karamertzanis Cc: CHEMISTRY@ccl.net Subject: CCL:Gamess question Hi, Gamess units are Atomic Units o Hartrees, indicated also as AU 1 AU is equivalent to: 27.2107 eV 4.35943E-11 erg 6.27503E+2 Kcal/mol 6.57966E+15 Hz 2.19474E+05 cm-1 3.15777E+05 K Cheers Alessandro Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltą di Farmacia Universitą degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm On Tue, 15 Oct 2002, Panagiotis G. Karamertzanis wrote: > Dear all, > > I started using GAMESS recently. I am computing electrostatic potential to > do later on fitting with distributed charges. > > The problem is that I do not know the units of the output of the GAMESS run. > The manual does not help with this. > > Thanks, > > Panagiotis Karamertzanis > CPSE Imperial College > > > > > > > > -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Oct 17 06:04:36 2002 Received: from hotmail.com ([64.4.21.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HA4Zf18922 for ; Thu, 17 Oct 2002 06:04:36 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 17 Oct 2002 03:04:32 -0700 Received: from 137.189.4.4 by lw14fd.law14.hotmail.msn.com with HTTP; Thu, 17 Oct 2002 10:04:32 GMT X-Originating-IP: [137.189.4.4] From: "Wing Lok Abe Kurtz Chiu" To: CHEMISTRY@ccl.net Subject: AIMPAC compled in Redhat 7.0 Date: Thu, 17 Oct 2002 18:04:32 +0800 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 17 Oct 2002 10:04:32.0870 (UTC) FILETIME=[9716F860:01C275C4] Hi, I have recently downloaded the AIMPAC software and found the diffculites to complie the source. Does anyone have the "cleaned" source codes and can send them to me? Any suggestion is welocmed. Thanks in advance. Best Regards. Kurtz Chiu Department of Chemistry The Chinese University of Hong Kong Hong Kong SAR, China _________________________________________________________________ Get a speedy connection with MSN Broadband.  Join now! http://resourcecenter.msn.com/access/plans/freeactivation.asp From chemistry-request@server.ccl.net Thu Oct 17 11:52:22 2002 Received: from relay3.softcomca.com ([168.144.1.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HFqMf27790 for ; Thu, 17 Oct 2002 11:52:22 -0400 Received: from M2W042.mail2web.com ([168.144.108.42]) by relay3.softcomca.com with Microsoft SMTPSVC(5.0.2195.5329); Thu, 17 Oct 2002 11:52:14 -0400 Message-ID: <54360-2200210417155214676@M2W042.mail2web.com> X-Priority: 3 Reply-To: nepenthes@vplaces.net X-Originating-IP: 161.142.100.85 X-URL: http://mail2web.com/ From: "nepenthes@vplaces.net" To: chemistry@ccl.net Subject: docking ligand to mutant protein Date: Thu, 17 Oct 2002 11:52:14 -0400 MIME-Version: 1.0 Content-type: text/plain; charset=iso-8859-1 X-OriginalArrivalTime: 17 Oct 2002 15:52:14.0668 (UTC) FILETIME=[29B0B8C0:01C275F5] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g9HFqMf27791 Dear All, When using Autodock3.0 to dock a ligand to a mutant protein, the estimated free energy of binding and also hydrogen bonds detected indicate that the ligand will bind to the mutant but experimental work has shown that it does not. I have used the same procedure to dock the same ligand to the wild-type protein and the result was consistent with experimental results. My mutant protein was prepared from the wild-type crystal structure (changed the residues using insightII). I'd like to ask whether anyone has encountered such a problem before. Could it be that the mutant protein structure was not suitable? An idea was proposed that the overall charge of the mutant and wild-type protein should remain the same, therefore, if the net charge for the mutant is less, then some residues should be mutated in order to obtain the same net charge as the wild-type protein. I'd appreciate any suggestions/feedback. Thank you all for your time. Kind regards, Rowyna -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From chemistry-request@server.ccl.net Thu Oct 17 10:11:59 2002 Received: from electra.cc.umanitoba.ca ([130.179.16.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HEBxf23930 for ; Thu, 17 Oct 2002 10:11:59 -0400 Received: from hultin (hultin.chem.umanitoba.ca [130.179.48.60]) by electra.cc.umanitoba.ca (8.12.3/8.12.3) with SMTP id g9HEBsJ9016723 for ; Thu, 17 Oct 2002 09:11:54 -0500 (CDT) From: "Phil Hultin" To: "Computational Chemistry List" Subject: Gaussian IRC Downhill Date: Thu, 17 Oct 2002 09:11:55 -0500 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0116_01C275BD.3CF67A10" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 Importance: Normal X-DCC-UofM-Metrics: electra 1032; IP=ok Body=1 Fuz1=1 Fuz2=1 This is a multi-part message in MIME format. ------=_NextPart_000_0116_01C275BD.3CF67A10 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit I am trying to use the Gaussian 98 "IRC=Downhill" keyword for the first time, and the program tells me that there is a syntax error caused by the "dowhill" option. Does anyone have any information about doing this properly? Input file: %chk=/extra1/gaussian/hultin/galOMeTS_recheck.chk %nprocs=8 #p B3LYP/6-31+G(d,p) IRC=(RCFC,Downhill,Maxpoints=150,Stepsize=5) <...Cartesian coordinate molecule specification...> Dr. Philip G. Hultin Associate Department Head and Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin@cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ ------=_NextPart_000_0116_01C275BD.3CF67A10 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
I am = trying to use=20 the Gaussian 98 "IRC=3DDownhill" keyword for the first time, and the = program tells=20 me that there is a syntax error caused by the "dowhill" option.  = Does=20 anyone have any information about doing this = properly?
 
Input=20 file:
 
%chk=3D/extra1/gaussian/hultin/galOMeTS_rechec= k.chk
%nprocs=3D8
 
#p = B3LYP/6-31+G(d,p)=20 IRC=3D(RCFC,Downhill,Maxpoints=3D150,Stepsize=3D5)    = ;    =20
 
<...Cartesian=20 coordinate molecule specification...>

Dr. Philip G. Hultin
Associate Department Head=20 and
Associate Professor of Chemistry
University of = Manitoba
Winnipeg,=20 MB, Canada R3T 2N2
(vox) 204-474-9814
(fax) 204-474-7608
mailto:hultin@cc.umanitoba.ca<= BR>http://www.umanitoba.ca/chemistry/

 
------=_NextPart_000_0116_01C275BD.3CF67A10-- From chemistry-request@server.ccl.net Thu Oct 17 05:24:38 2002 Received: from agnostix.bangor.ac.uk ([147.143.2.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9H9Obf18230 for ; Thu, 17 Oct 2002 05:24:37 -0400 Received: from scientifix.bangor.ac.uk (scientifix [147.143.2.119]) by agnostix.bangor.ac.uk (8.12.1/8.12.1) with ESMTP id g9H9OVXG005281 for ; Thu, 17 Oct 2002 10:24:31 +0100 (BST) Received: from belimawr (chem93 [147.143.16.34]) by scientifix.bangor.ac.uk (8.12.2+Sun/8.12.1) with SMTP id g9H9ODSb022359 for ; Thu, 17 Oct 2002 10:24:31 +0100 (BST) Message-ID: <003b01c275bf$9cbed2b0$22108f93@belimawr> From: "Helen Howard-Jones" To: Subject: gamess input $DATA error Date: Thu, 17 Oct 2002 10:28:36 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0038_01C275C7.F3D6D680" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_0038_01C275C7.F3D6D680 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I am having problems with inputting into gamess, after submitting the = benzene job below: $CONTRL COORD=3DCART UNITS=3DANGS scftyp=3DROB3LYP runtyp=3Doptimize = chrg=3D0 mult=3D1 $END $basis Gbasis=3D31 nauss=3D6 ndfunc=3D1 polar=3D1 $END $DATA optimisation of benzene:rob3lyp cnv naxis=3D6 C 6.0 1.40304 0.00000 0.00000 C 6.0 0.70011 1.21751 0.00000 C 6.0 -0.68795 1.21751 0.00000 C 6.0 -1.39034 0.00092 0.00000 C 6.0 -0.68873 -1.21431 0.00000 C 6.0 0.69814 -1.21431 0.00000 H 1.0 2.48465 0.00000 0.00000 H 1.0 1.24065 2.15375 0.00000 H 1.0 -1.37005 2.39894 0.00000 H 1.0 -2.47209 0.00092 0.00000 H 1.0 -1.22991 -2.15166 0.00000 H 1.0 1.23711 -2.15294 0.00000 $END $SCF dirscf=3D.true.$end which the job submits but then crashes out giving the error no $DATA = group, I am also wanting to submit a structure with dummy atoms also and = usually run jobs in internal coors (in G98w) any help is gratefully = received. Helen ------=_NextPart_000_0038_01C275C7.F3D6D680 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
I am having problems with inputting = into gamess,=20 after submitting the benzene job below:
 
$CONTRL COORD=3DCART UNITS=3DANGS = scftyp=3DROB3LYP=20 runtyp=3Doptimize chrg=3D0
mult=3D1 $END $basis Gbasis=3D31 nauss=3D6 = ndfunc=3D1 polar=3D1=20 $END
$DATA
optimisation of benzene:rob3lyp
cnv=20 naxis=3D6
C    6.0     = 1.40304  =20 0.00000   0.00000
C    = 6.0    =20 0.70011   1.21751   0.00000
C   =20 6.0    -0.68795   1.21751  =20 0.00000
C    6.0    = -1.39034  =20 0.00092   0.00000
C    6.0    = -0.68873  -1.21431   0.00000
C   =20 6.0     0.69814  -1.21431  =20 0.00000
H    1.0     = 2.48465  =20 0.00000   0.00000
H    = 1.0    =20 1.24065   2.15375   0.00000
H   =20 1.0    -1.37005   2.39894  =20 0.00000
H    1.0    = -2.47209  =20 0.00092   0.00000
H    1.0    = -1.22991  -2.15166   0.00000
H   =20 1.0     1.23711  -2.15294  =20 0.00000
$END
$SCF dirscf=3D.true.$end
 
which the job submits but then crashes = out giving=20 the error no $DATA group, I am also wanting to submit a structure with = dummy=20 atoms also and usually run jobs in internal coors (in G98w) = any help=20 is gratefully received.
 
Helen
------=_NextPart_000_0038_01C275C7.F3D6D680-- From chemistry-request@server.ccl.net Wed Oct 16 19:25:04 2002 Received: from mxout2.cac.washington.edu ([140.142.33.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9GNP3f28684 for ; Wed, 16 Oct 2002 19:25:04 -0400 Received: from mailscan-out2.cac.washington.edu (mailscan-out2.cac.washington.edu [140.142.33.17]) by mxout2.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.09) with SMTP id g9GNP3OZ020793 for ; Wed, 16 Oct 2002 16:25:04 -0700 Received: FROM smtp.washington.edu BY mailscan-out2.cac.washington.edu ; Wed Oct 16 16:25:01 2002 -0700 Received: from donald ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW01.12/8.12.1+UW02.08) with SMTP id g9GNP1qj017407 for ; Wed, 16 Oct 2002 16:25:01 -0700 Message-ID: <006801c2756a$fc9372e0$74805f80@donald> From: "Carsten Detering" To: Subject: charges on receptor and docking Date: Thu, 17 Oct 2002 01:23:08 +0200 Organization: University of Washington MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0065_01C2757B.BFF7A3E0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0065_01C2757B.BFF7A3E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello everybody, my following question might have a straightforward answer, however, it = is important to me and I havent found a satisfying answer yet. When going through the literature, people are using Kollman united atom charges on target molecules for docking most of the time. What is the = reason for that? Because, for my example complexes (RNA-small molecule), this is = not the optimal force field. Binding constants are computed much to = strong as compared to the experimental values. With Gasteiger charges or = the CFF91 force field (InsightII) for my receptors, the results look = much better. (Gasteiger charges I compute with Vega - thanks to Prof. = Vistoli at this point). I would appreciate any comments on that. Thanks a lot in advance, Carsten detering@u.washington.edu=20 ------=_NextPart_000_0065_01C2757B.BFF7A3E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello=20 everybody,

my following question might have a straightforward = answer,=20 however, it is important to me and I havent found a satisfying = answer=20 yet.
When going through the literature, people are using Kollman = united=20 atom
charges on target molecules for docking most of the time. What = is the=20 reason for
that? Because, for my example complexes (RNA-small = molecule), this=20 is not the optimal force field. Binding constants are computed much to = strong as=20 compared to the experimental values. With Gasteiger charges or the CFF91 = force=20 field (InsightII) for my receptors, the results look much better.=20 (Gasteiger charges I compute with Vega - thanks to Prof. Vistoli at this = point).

I would appreciate any comments on that. Thanks a lot in=20 advance,

Carsten
 
detering@u.washington.edu=20


 
------=_NextPart_000_0065_01C2757B.BFF7A3E0-- From chemistry-request@server.ccl.net Thu Oct 17 12:43:53 2002 Received: from meta4.mbasis.com ([216.98.157.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HGhrf29416 for ; Thu, 17 Oct 2002 12:43:53 -0400 Received: by meta4.mbasis.com with Internet Mail Service (5.5.2656.59) id <4WQTRLF0>; Thu, 17 Oct 2002 09:42:17 -0700 Message-ID: From: Rami Reddy To: chemistry@ccl.net Subject: Computer programs for estimating pKa values of small values Date: Thu, 17 Oct 2002 09:42:08 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: text/plain; charset="iso-8859-1" We are looking for a computer program for estimating pKa values of small molecules (MW<500). If you know any good computer program(s), please let me know ASAP with all the details. Thanks, M. Rami Reddy Tel: (858)-622-3967 Emal: reddy@mbasis.com From chemistry-request@server.ccl.net Thu Oct 17 13:00:14 2002 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HH0Df29734 for ; Thu, 17 Oct 2002 13:00:13 -0400 Received: from daveg.cachesoftware.com ([192.168.110.100]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id g9HGx7t22421; Thu, 17 Oct 2002 09:59:07 -0700 Message-Id: <5.1.0.14.0.20021017094507.02b406e0@pop3.norton.antivirus> X-Sender: daveg/mail.cachesoftware.com@pop3.norton.antivirus X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 17 Oct 2002 09:58:20 -0700 To: Antonio Fernandez From: David Gallagher Subject: Re: CCL:AM1/PM3 parameters for copper Cc: chemistry@ccl.net In-Reply-To: <02101709444101.32317@antonio> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_6674359==_.ALT" --=====================_6674359==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Antonio, MOPAC 2000 and later versions handle Copper with AM1-d. The latest version of CAChe MOPAC 2002 includes parameters for Sc, Ti, V, Cr, Fe, Co, Ni, Cu, Zr, Mo, Pd, Ag, and Pt for all three methods, PM5, AM1 and PM3. However, the parameters would not work in earlier versions of MOPAC without the latest d-orbital code modifications. You can evaluate the latest version of MOPAC 2002 by downloading the CAChe WorkSystem version 5.04 from http://www.cachesoftware.com/cache/cachedemo_win.shtml David Gallagher, CAChe Group, Fujitsu At 09:44 AM 10/17/2002 -0400, Antonio Fernandez wrote: >Hi, >Does anyone know where could I get the AM1 and/or PM3 parameters for copper? >If any, I would like to implement them in MOPAC7.0. > >Antonio. > >-- >Antonio Fernandez Ramos >Dpto de Quimica Fisica >Facultade de Quimica >Universidade de Santiago de Compostela >15706 Santiago de Compostela >Spain >E-mail: qftramos@usc.es > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net --=====================_6674359==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Antonio,

MOPAC 2000 and later versions handle Copper with AM1-d. The latest version of CAChe MOPAC 2002 includes parameters for Sc, Ti, V, Cr, Fe, Co, Ni, Cu, Zr, Mo, Pd, Ag, and Pt for all three methods, PM5, AM1 and PM3. However, the parameters would not work in earlier versions of MOPAC without the latest d-orbital code modifications.

You can evaluate the latest version of MOPAC 2002 by downloading the CAChe WorkSystem version 5.04 from http://www.cachesoftware.com/cache/cachedemo_win.shtml
           
David Gallagher, CAChe Group, Fujitsu


At 09:44 AM 10/17/2002 -0400, Antonio Fernandez wrote:
Hi,
Does anyone know where could I get the AM1 and/or PM3 parameters for copper?
If any, I would like to implement them in MOPAC7.0.

Antonio.

--
Antonio Fernandez Ramos
Dpto de Quimica Fisica
Facultade de Quimica
Universidade de Santiago de Compostela
15706 Santiago de Compostela
Spain
E-mail: qftramos@usc.es

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--=====================_6674359==_.ALT-- From chemistry-request@server.ccl.net Thu Oct 17 15:31:53 2002 Received: from postal.sdsc.edu ([132.249.20.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HJVqf32653 for ; Thu, 17 Oct 2002 15:31:52 -0400 Received: from koa.sdsc.edu (IDENT:g+6/aJOCLHVGMzG1LqX0AlPkRi4dAiot@koa.sdsc.edu [132.249.23.116]) by postal.sdsc.edu (8.11.6/8.11.6/server/48) with ESMTP id g9HJVpv24606; Thu, 17 Oct 2002 12:31:52 -0700 (PDT) Received: from localhost by koa.sdsc.edu (SGI-8.9.3/1.11-IRIXclient) with ESMTP id MAA08485; Thu, 17 Oct 2002 12:31:50 -0700 (PDT) Date: Thu, 17 Oct 2002 12:31:50 -0700 From: Wibke Sudholt To: Rami Reddy cc: Subject: Re: CCL:Computer programs for estimating pKa values of small values In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, perhaps try Jaguar: http://www.schrodinger.com/Products/pka.html Kind regards, Dr. Wibke Sudholt University of California, San Diego On Thu, 17 Oct 2002, Rami Reddy wrote: > We are looking for a computer program for estimating pKa values of small > molecules (MW<500). If you know any good computer program(s), please let me > know ASAP with all the details. > > Thanks, > M. Rami Reddy > Tel: (858)-622-3967 > Emal: reddy@mbasis.com > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net