From chemistry-request@ccl.net Mon Aug 25 08:22:14 2003 Received: from pat.uio.no (pat.uio.no [129.240.130.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7PCMDYj020622 for ; Mon, 25 Aug 2003 08:22:14 -0400 Received: from mail-mx5.uio.no ([129.240.10.46]) by pat.uio.no with esmtp (Exim 4.20) id 19rGMO-0000Hr-BH for chemistry|at|ccl.net; Mon, 25 Aug 2003 14:22:12 +0200 Received: from snapp.uio.no ([129.240.130.64]) by mail-mx5.uio.no with esmtp (Exim 4.14) id 19rGMJ-0007jQ-2A for chemistry|at|ccl.net; Mon, 25 Aug 2003 14:22:07 +0200 Received: from bio89162.uio.no ([129.240.89.162] helo=bio89162.ulrik.uio.no) by snapp.uio.no with esmtp (Exim 2.12 #7) id 19rGM8-0001dz-00 for chemistry|at|ccl.net; Mon, 25 Aug 2003 14:21:56 +0200 Message-Id: <5.1.0.14.2.20030825141943.00b44ee8|at|uio-pop.uio.no> X-Sender: sergioma|at|uio-pop.uio.no X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 25 Aug 2003 14:20:09 +0200 To: chemistry|at|ccl.net From: Sergio Manzetti Subject: Autodock Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed X-MailScanner-Information: This message has been scanned for viruses/spam. Contact postmaster|at|uio.no if you have questions about this scanning. X-UiO-MailScanner: No virus found Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h7PCMEYj020623 Hi, I wanted to ask a question to confirm the following: When I dock testosterone on a protein, I choose the crucial atom in the active site as the center of the grid (in the macro.gpf file) and as the center to move and rotate about in the lig.macro.dpf file. Still the ligand results very far away from this position (up to 8 E) separated by maybe 10 cubic E of vacuum. Am i doing something very wrong here? Thanks Sergio From chemistry-request@ccl.net Mon Aug 25 06:46:58 2003 Received: from smtp.hotbox.ru (smtp.hotbox.ru [80.68.244.50]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7PAkvYj018887 for ; Mon, 25 Aug 2003 06:46:58 -0400 Received: from verena.ineos.ac.ru (verena.ineos.ac.ru [193.233.4.18]) (authenticated bits=0) by smtp.hotbox.ru (8.12.9/8.12.9) with ESMTP id h7PAXerB057105 for ; Mon, 25 Aug 2003 14:33:40 +0400 (MSD) (envelope-from dengolovanov|at|pisem.net) Date: Mon, 25 Aug 2003 14:54:15 +0400 From: dengolovanov X-Mailer: The Bat! (v1.61) Reply-To: dengolovanov X-Priority: 3 (Normal) Message-ID: <79403385147.20030825145415|at|pisem.net> To: chemistry|at|ccl.net Subject: Re[2]: CCL:Spin-Spin Coupling Constants In-Reply-To: <20030825123711.A275494|at|compchem.dfh.dk> References: <3275164520.20030820121434|at|pisem.net> <20030825123711.A275494|at|compchem.dfh.dk> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Jeremy, Monday, August 25, 2003, 2:37:11 PM, you wrote: >> Dear CCL's >> Thank's every one who helped me with NICS question, but another one >> question about NMR calculations occured. >> Recenly Cremer have proposed a scheme which can be used for calculations of Spin-Spin >> Coupling Constants and I heared that it's a good approach in the case >> of simple organic molecules within DFT calculations. >> Unfortunately my background is not sufficient to find out how to carry >> out this within Gaussian. JRG> It's built-in if you have g03. JRG> nmr=spinspin JRG> J. JRG> ---------------------------------------------------------------------- JRG> Jeremy Greenwood jeremy|at|greenwood.net JRG> Department of Medicinal Chemistry bh +45 35306117 JRG> The Danish University of Pharmaceutical Sciences fx +45 35306040 JRG> Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 JRG> ---------------------------------------------------------------------- No I don't have G03 program package. As I suppose Cremer used G98 program. -- Best regards, Denis G. Golovanov mailto:dengolovanov|at|pisem.net From chemistry-request@ccl.net Mon Aug 25 03:16:36 2003 Received: from socrates.cc.uoi.gr (socrates.cc.uoi.gr [195.130.119.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7P7GZYj012368 for ; Mon, 25 Aug 2003 03:16:36 -0400 Received: from prokopis (pc232.chem.uoi.gr [195.130.116.232]) by socrates.cc.uoi.gr (8.9.3/8.9.3) with SMTP id KAA09184 for ; Mon, 25 Aug 2003 10:09:32 +0300 (EEST) Message-ID: <001401c36ad8$ce78a880$e87482c3@prokopis> From: "George Papamokos" To: Subject: CCL Re to H-Bond Calculated energies Date: Mon, 25 Aug 2003 10:15:59 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C36AF1.E18072A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C36AF1.E18072A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Huajun, Try=20 J. Chem. Phys., 114, 3949 [ 2001].=20 J. Phys. Chem., 106, 356 [2002]. J. Phys. Chem., 105, 4470 [2001]. J. Am. Chem. Soc., 123, 4255 [2001]. George Papamokos Ph. D. student Ioannina University Greece ------=_NextPart_000_0009_01C36AF1.E18072A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi Huajun,
 
Try
J. Chem. Phys.,  = 114, =20 3949 [ 2001]. 
J.  Phys. Chem.,  = 106,=20 356   [2002].
J. Phys. Chem., 105, 4470  =20 [2001].
J. Am. Chem. Soc., 123,=20 4255 [2001].
 
 
George Papamokos
Ph. D. student
 
Ioannina University
Greece
------=_NextPart_000_0009_01C36AF1.E18072A0-- From chemistry-request@ccl.net Mon Aug 25 14:45:51 2003 Received: from kafka.net.nih.gov (kafka.net.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7PIjoYj001039 for ; Mon, 25 Aug 2003 14:45:50 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.9/8.12.9) with ESMTP id h7PIjlx9014390 for ; Mon, 25 Aug 2003 14:45:47 -0400 (EDT) Date: Mon, 25 Aug 2003 14:04:15 -0400 From: Rick Venable To: chemistry^at^ccl.net Subject: CCL: using MMFF in CHARMM In-Reply-To: Message-ID: References: ReplyTo: Rick_Venable^at^nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I'm having some problems using MMFF (Merck Molecular Force Field) in CHARMM, when trying to import a PDB file with multiple molecules. Using GENERATE more than once doesn't seem to work, and if I try to read everything at once the C-term patching of the protein gets screwed up. I'd appreciate suggestions from anyone with experience using MMFF (or CFF, for that matter) for an enzyme with a drug in the active site. Regards, =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable^at^nih.gov ALT email: rvenable^at^speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Mon Aug 25 15:57:23 2003 Received: from mail1.engr.sc.edu (mail1.engr.sc.edu [129.252.21.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7PJvNYj003379 for >ccl.net>; Mon, 25 Aug 2003 15:57:23 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6375.0 Subject: formchk problem Date: Mon, 25 Aug 2003 15:57:22 -0400 Message-ID: <99296F29E0A01A40A0503EB30507ECF91E9A58<>mail1.engr.sc.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: formchk problem Thread-Index: AcNrQxk+5SgyycI8T1quu/Rd3wahCg== From: "WANG, YIXUAN " >engr.sc.edu> To: >ccl.net> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h7PJvNYj003380 Dear CCL-ers, We are trying to convert a check point file of a medium-size system (>150 atoms, basis functions ~2000) into a formatted form with formchk. The error message reads formchk e300.chk> Read checkpoint file e300.chk Write formatted file e300.fchk FChkPn allocation failure: iend,mxcore= 3944196 2999478 Error termination via Lnk1e. forrtl: severe (174): SIGSEGV, segmentation fault occurred cannot read in formchk as I understand it may be due to the default memory of formchk is not enough, since it really works well for small systems. Whatever causes it, could somebody have an idea to solve it? Thanks in advance. Yixuan Chem. Engineering Univ. South Carolina From chemistry-request@ccl.net Mon Aug 25 11:07:43 2003 Received: from web21101.mail.yahoo.com (web21101.mail.yahoo.com [216.136.227.103]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h7PF7gYj027584 for >ccl.net>; Mon, 25 Aug 2003 11:07:42 -0400 Message-ID: <20030825150741.14819.qmail<>web21101.mail.yahoo.com> Received: from [203.197.89.222] by web21101.mail.yahoo.com via HTTP; Mon, 25 Aug 2003 08:07:41 PDT Date: Mon, 25 Aug 2003 08:07:41 -0700 (PDT) From: Gurpreet Singh >yahoo.com> Subject: CCL: Titanium To: chemistry<>ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-676722814-1061824061=:14530" --0-676722814-1061824061=:14530 Content-Type: text/plain; charset=us-ascii Dear CCLers, In G98W, What basis sets can be used for Titanium ? I was told that the LanL2DZ basis was appropiate but many times the scf does not converge when I turn it on. The same calculation runs perfectly for a lower basis set on all atoms. The input file is attached. Thank you, Gurpreet Singh NMR Div, NCL, Pune , India >>>>>>>>>> Convergence criterion not met. SCF Done: E(RHF) = -5284.36805666 A.U. after 65 cycles Convg = 0.6382D-03 -V/T = 2.0051 S**2 = 0.0000 KE= 5.257501392216D+03 PE=-2.745297553393D+04 EE= 9.537873151299D+03 Convergence failure -- run terminated. Error termination via Lnk1e in h:\G98W\l502.exe --------------------------------------------------------------------------- Input file --------------------------------------------------------------------------------- %mem=250mb %chk=et_01.chk #p nmr hf/3-21g prop=efg Iop33(10=1) Extrabasis ets10 site 6 nmr -4 1 H 3.103734732 5.987514973 6.778284073 TI 7.886360168 10.500499725 6.767665386 TI 5.253900528 7.879365444 6.647471905 H 9.782996178 12.649885178 6.902834892 H 6.275192261 14.092790604 9.818439484 SI 2.954096079 9.744250298 5.233300209 H 0.384500682 10.893193245 11.607704163 SI 6.026371479 12.764617920 5.322904110 H 3.023486614 8.278820992 11.704815865 H 9.439110756 8.705522537 8.162964821 H 6.811385632 6.007072926 5.370864391 H 2.960453272 13.505114555 1.702411890 H 0.346313775 7.495884895 8.470077515 SI 3.429080725 10.216356277 8.012237549 H 5.646386623 10.835413933 1.600062847 SI 5.585982323 12.375048637 8.106037140 H 9.720950127 8.940502167 5.458132267 H 7.105151653 6.400471687 8.067461014 H 7.768979549 14.580838203 5.253762722 H 1.101265550 8.016464233 5.198528767 SI 1.374871016 9.213978767 10.019799232 SI 3.989010811 11.787021637 3.252134085 O 3.084014177 10.804594040 4.086316109 O 0.469874352 10.196405411 10.853981018 O 4.239344120 8.808654785 5.355118275 O 2.807680130 10.480128288 6.600233555 O 1.662942290 8.848347664 4.967466354 O 4.908683777 12.642601967 4.213819027 O 2.294543982 8.358397484 10.981483459 O 6.895724773 11.437144279 5.462859631 O 8.876994133 9.563855171 8.072471619 O 5.364562988 13.026500702 6.704590797 O 6.192787170 6.829734325 5.409123898 O 6.856696129 8.906942368 6.614851475 O 8.916023254 12.094055176 6.920479298 O 3.655379295 6.857245445 6.790810585 O 5.707406044 13.499653816 9.196580887 O 4.317677975 8.899803162 7.910453320 O 6.249120712 6.963720322 7.963241577 O 6.904240131 11.484816551 8.024419785 O 8.868480682 9.516183853 5.510910511 O 4.342586517 11.446383476 8.441849709 O 2.268520117 10.067877769 9.051887512 O 4.882659912 10.933123589 2.284222364 O 6.983282566 13.979946136 4.966518879 O 0.454722732 8.229452133 9.184938431 O 3.068862438 12.771547318 2.417273045 2 3 0 LanL2DZ **** --------------------------------- Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software --0-676722814-1061824061=:14530 Content-Type: text/html; charset=us-ascii

Dear CCLers,

                    In G98W, What basis sets can be used for Titanium ? I was told that the LanL2DZ basis was appropiate but many times the scf does not converge when I turn it on.

The same calculation runs perfectly for a lower basis set on all atoms.

The input file is attached.

Thank you,

Gurpreet Singh

NMR Div, NCL, Pune , India 

>>>>>>>>>> Convergence criterion not met.

SCF Done: E(RHF) = -5284.36805666 A.U. after 65 cycles

Convg = 0.6382D-03 -V/T = 2.0051

S**2 = 0.0000

KE= 5.257501392216D+03 PE=-2.745297553393D+04 EE= 9.537873151299D+03

Convergence failure -- run terminated.

Error termination via Lnk1e in h:\G98W\l502.exe

---------------------------------------------------------------------------

Input file

---------------------------------------------------------------------------------

%mem=250mb
%chk=et_01.chk
#p nmr hf/3-21g prop=efg Iop33(10=1) Extrabasis

ets10 site 6
nmr

-4 1
H      3.103734732    5.987514973    6.778284073
TI     7.886360168   10.500499725    6.767665386
TI     5.253900528    7.879365444    6.647471905
H      9.782996178   12.649885178    6.902834892
H      6.275192261   14.092790604    9.818439484
SI     2.954096079    9.744250298    5.233300209
H      0.384500682   10.893193245   11.607704163
SI     6.026371479   12.764617920    5.322904110
H      3.023486614    8.278820992   11.704815865
H      9.439110756    8.705522537    8.162964821
H      6.811385632    6.007072926    5.370864391
H      2.960453272   13.505114555    1.702411890
H      0.346313775    7.495884895    8.470077515
SI     3.429080725   10.216356277    8.012237549
H      5.646386623   10.835413933    1.600062847
SI     5.585982323   12.375048637    8.106037140
H      9.720950127    8.940502167    5.458132267
H      7.105151653    6.400471687    8.067461014
H      7.768979549   14.580838203    5.253762722
H      1.101265550    8.016464233    5.198528767
SI     1.374871016    9.213978767   10.019799232
SI     3.989010811   11.787021637    3.252134085
O      3.084014177   10.804594040    4.086316109
O      0.469874352   10.196405411   10.853981018
O      4.239344120    8.808654785    5.355118275
O      2.807680130   10.480128288    6.600233555
O      1.662942290    8.848347664    4.967466354
O      4.908683777   12.642601967    4.213819027
O      2.294543982    8.358397484   10.981483459
O      6.895724773   11.437144279    5.462859631
O      8.876994133    9.563855171    8.072471619
O      5.364562988   13.026500702    6.704590797
O      6.192787170    6.829734325    5.409123898
O      6.856696129    8.906942368    6.614851475
O      8.916023254   12.094055176    6.920479298
O      3.655379295    6.857245445    6.790810585
O      5.707406044   13.499653816    9.196580887
O      4.317677975    8.899803162    7.910453320
O      6.249120712    6.963720322    7.963241577
O      6.904240131   11.484816551    8.024419785
O      8.868480682    9.516183853    5.510910511
O      4.342586517   11.446383476    8.441849709
O      2.268520117   10.067877769    9.051887512
O      4.882659912   10.933123589    2.284222364
O      6.983282566   13.979946136    4.966518879
O      0.454722732    8.229452133    9.184938431
O      3.068862438   12.771547318    2.417273045

2 3 0
LanL2DZ
****

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Yahoo! SiteBuilder - Free, easy-to-use web site design software --0-676722814-1061824061=:14530-- From chemistry-request@ccl.net Mon Aug 25 18:11:14 2003 Received: from mail.interware.hu ([195.70.32.156]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7PMBDYj007485 for >ccl.net>; Mon, 25 Aug 2003 18:11:14 -0400 Received: from caracas-0616.adsl.interware.hu ([213.178.102.104] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.20 #1 (Debian)) id 19rPYP-00034X-EK for >ccl.net>; Tue, 26 Aug 2003 00:11:13 +0200 Message-ID: <002b01c36b5e$3cd166c0$0200a8c0@cthulhu> From: "Tamas E. Gunda" >tigris.unideb.hu> To: >ccl.net> Subject: CCL: Mol2Mol 5.1.1 Date: Tue, 26 Aug 2003 00:11:20 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Dear CCL Members, The new 5.1.1 version of the molecule file conversion, manipulation and utility program Mol2Mol is now available > from http://web.interware.hu/frenzy/mol2mol as trial or shareware version. The current version of Mol2Mol recognizes, and interconverts more than 40 different file formats (including subtypes). It can slice multiple structural files to single ones (such as PDB models or MDL SD files to single ones) and vice versa in several variations. Support for PDB Chime subformat (with 1-2-3 bonds). New in Mol2Mol 5.1: New file type: Maestro file type added (read/write, compressed/uncompressed, single/multi) Support of MacroModel atomtypes extended according to version 8.1 Display: Option to display hetero atom and hydrogen atom symbols in vector models. Option added for chosing the anaglyph stereo colors: red/green or red/blue. Several improvements concerning 2D molfiles (ISIS/Draw mol, sdf, rxn, rdf, ChemDraw ct, WinPLT): Implicit hydrogens are added and optionally shown. In the case of 2D molfiles stereobonds are now displayed. Atom aliases from ISIS/Draw files and ChemDraw ct files are displayed and are mutually converted. When converting to WinPLT files, implicit hydrogen support has been enhanced, conversion of atom aliases is also supported. and several bug fixes. Mol2Mol is a very handy set of tools for everybody dealing with molecular modelling. It is impossible to write here all of the features of Mol2Mol, but have a look at its home page: http://web.interware.hu/frenzy/mol2mol POV-Ray fans may also have a look at: http://dragon.klte.hu/~gundat/povraya.htm The program is available as 30 days unrestricted trial version or as shareware version. Dr. Tamas E. Gunda tamasgunda*AT*tigris.klte.hu