From chemistry-request@server.ccl.net Wed Feb 19 00:08:37 2003 Received: from mail.hybrid.fi ([195.170.158.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1J58aI17311 for ; Wed, 19 Feb 2003 00:08:37 -0500 Received: (from localhost user: 'markku', uid#1889) by hybrid.fi with ESMTP id ; Wed, 19 Feb 2003 07:08:11 +0200 Date: Wed, 19 Feb 2003 07:08:11 +0200 (EET) Sender: Markku Laukkanen From: Markku Laukkanen X-Sender: markku@hybrid.fi To: chemistry@ccl.net Subject: Generating conformations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Is there any known free or low cost program generate low energy conformations for given molecule to use in docking experiments? Any help is appreciated! Thx, PKY From chemistry-request@server.ccl.net Wed Feb 19 05:23:42 2003 Received: from darius.ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1JANeI03163 for ; Wed, 19 Feb 2003 05:23:41 -0500 Received: from echo.ribotargets.com (echo [194.129.39.91]) by darius.ribotargets.com (SGI-8.9.3/8.9.3) with ESMTP id KAA46340; Wed, 19 Feb 2003 10:35:06 GMT Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18lRJc-00019L-00; Wed, 19 Feb 2003 10:19:00 +0000 Date: Wed, 19 Feb 2003 10:19:00 +0000 (GMT) From: Szilveszter Juhos To: Markku Laukkanen cc: chemistry@ccl.net Subject: Re: CCL:Generating conformations In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 19 Feb 2003, Markku Laukkanen wrote: > Is there any known free or low cost program generate low energy > conformations for given molecule to use in docking experiments? Try: GOLD: http://www.ccdc.cam.ac.uk/prods/gold/ FlexX: http://cartan.gmd.de/flexx/ AutoDock: http://www.scripps.edu/pub/olson-web/doc/autodock/index.html Glide: http://www.schrodinger.com/Products/glide.html (once their web server is back) Most of them have a demo version (or you can ask for). If you want to make more elaborate docking experiments, that is a problem :-/ For AI/data mining likely you need quite a few poses and a good knowledge of the target. Hope it helps: Szilva From chemistry-request@server.ccl.net Wed Feb 19 01:15:57 2003 Received: from pado.krict.re.kr ([203.250.2.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1J6FuI18074 for ; Wed, 19 Feb 2003 01:15:56 -0500 Received: from anakin ([203.250.4.112]) by pado.krict.re.kr (v3smtp 8.11.6.6/8.11.2) with ESMTP id h1J69vn00398 for ; Wed, 19 Feb 2003 15:09:57 +0900 From: =?ks_c_5601-1987?B?sejA5bno?= To: Subject: 2D to 3D converter Date: Wed, 19 Feb 2003 15:16:05 +0900 Message-ID: <000201c2d7de$62c822b0$7004facb@anakin> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0003_01C2D829.D2C3A0D0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0003_01C2D829.D2C3A0D0 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: 7bit Hi! Is there any known freeware program converting 2D molecular structure to 3D for given sd or sdf files? Any comment or information will be appreciated !! Regards, Jangbae * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Jangbae Kim Researcher Bio-Organic Science Division Korea Research Institute of Chemical Technology (KRICT) P.O.Box 107, Yuseong, Taejeon, 305-600, Korea TEL : +82-42-860-7067 FAX : +82-42-861-0307 E-mail : jbkim@krict.re.kr * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ------=_NextPart_000_0003_01C2D829.D2C3A0D0 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable

Hi!

 

Is there any known freeware program converting 2D molecular = structure to 3D for given sd = or sdf files?

 

Any comment or information will be appreciated = !!

 

Regards,

 

Jangbae

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

Jangbae = Kim

Rese= archer           &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p; 

Bio-= Organic Science Division

Kore= a Research Institute of Chemical Technology (KRICT)

 

P.O.Box 107,  Yuseong, Taejeon,

305-= 600, Korea

TEL = : +82-42-860-7067

FAX = : +82-42-861-0307

E-ma= il : jbkim@krict.re.kr=

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

 

------=_NextPart_000_0003_01C2D829.D2C3A0D0-- From chemistry-request@server.ccl.net Wed Feb 19 03:53:16 2003 Received: from puga.vdu.lt ([193.219.38.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1J8rFI21119 for ; Wed, 19 Feb 2003 03:53:15 -0500 Received: from amavis by puga.vdu.lt with scanned-ok for chemistry@ccl.net id 18lPyO-0006HX-00; Wed, 19 Feb 2003 10:53:00 +0200 Received: from vaidila.vdu.lt ([193.219.38.52] ident=mail) by puga.vdu.lt with esmtp for chemistry@ccl.net id 18lPyO-0006HO-00; Wed, 19 Feb 2003 10:53:00 +0200 Received: from vejas.vdu.lt ([193.219.38.82] helo=localhost) by vaidila.vdu.lt with esmtp for chemistry@ccl.net id 18lQDd-0000An-00; Wed, 19 Feb 2003 11:08:45 +0200 Date: Wed, 19 Feb 2003 10:52:41 +0200 From: Arturas X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: Arturas Organization: SemteX X-Priority: 3 (Normal) Message-ID: <193412589722.20030219105241@vaidila.vdu.lt> To: CCL Subject: "graphical engines" in molecular visualisation & etc. ??? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS snapshot-20020300 Hello CCL, We are about to make some new software which need graphical interface to visualize molecules. Could anyone point to any related information about precompiled "graphical engines" or any related informations, algorithms, etc. which are useful? And the second: any literature or other resources about how construct molecular topology (amino acids, other compounds), rules interpreting connectivity in 3D models, etc. Very appreciate any help. Best regards, Arturas Z. mailto:a3arzi@vaidila.vdu.lt http://biologija.vdu.lt/person/ziemar/index.html From chemistry-request@server.ccl.net Wed Feb 19 05:46:02 2003 Received: from mail.hybrid.fi ([195.170.158.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1JAk1I03470 for ; Wed, 19 Feb 2003 05:46:01 -0500 Received: (from localhost user: 'markku', uid#1889) by hybrid.fi with ESMTP id convert rfc822-to-8bit; Wed, 19 Feb 2003 12:45:51 +0200 Date: Wed, 19 Feb 2003 12:45:51 +0200 (EET) Sender: Markku Laukkanen From: Markku Laukkanen X-Sender: markku@hybrid.fi To: Szilveszter Juhos cc: chemistry@ccl.net Subject: Re: CCL:Generating conformations In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8BIT On Wed, 19 Feb 2003, Szilveszter Juhos wrote: > On Wed, 19 Feb 2003, Markku Laukkanen wrote: > > Is there any known free or low cost program generate low energy > > conformations for given molecule to use in docking experiments? > > Try: > > GOLD: http://www.ccdc.cam.ac.uk/prods/gold/ > FlexX: http://cartan.gmd.de/flexx/ > AutoDock: http://www.scripps.edu/pub/olson-web/doc/autodock/index.html > Glide: http://www.schrodinger.com/Products/glide.html (once their web > server is back) > > Most of them have a demo version (or you can ask for). If you want to make > more elaborate docking experiments, that is a problem :-/ For AI/data > mining likely you need quite a few poses and a good knowledge of the > target. The problem is, that we have our own GA docking module, which is quite accurate and fast docking rigid/rigid pairs to known (5 -20 å radius) binding pocket. So I am not necessarely interested in evaluating one of those :-) But I would like to get a piece of software, where I could e.g. ask for 10000 least energy conformations (e.q. with certain energy margin as a difference) & dock those after that using GA & marginally flexible conformation instead. When I try to used totally flexible ligand and more than 20 rotors, it quite often happens, that the amount of conformations using torsion library to analyze the possible torsion angles for conformations exceed the limit of 32 bit integer :-) And the time to do the docking exceed the time for me to wait next to computer. I downloaded tinker and tried it ( thanks to Per-Ola Norrby ) , looks quite promising but would require more information how to use it. Also I would like to integrate everything with my c++ code piece. PKY From chemistry-request@server.ccl.net Wed Feb 19 08:17:05 2003 Received: from web13502.mail.yahoo.com ([216.136.175.81]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h1JDH4I05492 for ; Wed, 19 Feb 2003 08:17:04 -0500 Message-ID: <20030219131704.5604.qmail@web13502.mail.yahoo.com> Received: from [130.238.38.145] by web13502.mail.yahoo.com via HTTP; Wed, 19 Feb 2003 05:17:04 PST Date: Wed, 19 Feb 2003 05:17:04 -0800 (PST) From: Subject: FLO+ or QXP To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, I would like to know if anyone has used or uses flo > from Mcmartin. And the views about the program. Thanks ===== Yogesh Sabnis, PhDBox 574,Avd Org. Farm. Kemi,BMC, Husargatan 3,Uppsala - 75123Sweden __________________________________________________ Do you Yahoo!? Yahoo! Shopping - Send Flowers for Valentine's Day http://shopping.yahoo.com From chemistry-request@server.ccl.net Wed Feb 19 09:36:02 2003 Received: from chemik.chem.univ.gda.pl ([153.19.29.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1JEa1I07343 for ; Wed, 19 Feb 2003 09:36:02 -0500 Received: from localhost (maharan@localhost) by chemik.chem.univ.gda.pl (8.11.6+Sun/8.11.6) with ESMTP id h1JEXKT20055 for ; Wed, 19 Feb 2003 15:33:20 +0100 (CET) Date: Wed, 19 Feb 2003 15:33:20 +0100 (CET) From: Maciej Haranczyk To: chemistry@ccl.net Subject: ploting electron holes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello CCL, I would like to plot an electron hole (difference in electron density of neutral and cation at the same geometry) from Gaussian98 outputs. Do you know any software that can draw 2D or 3D picutes of electron holes ? Best wishes Maciek -- Maciek Haranczyk maharan@chem.univ.gda.pl From chemistry-request@server.ccl.net Wed Feb 19 10:23:31 2003 Received: from electra.cc.umanitoba.ca ([130.179.16.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1JFNVI08271 for ; Wed, 19 Feb 2003 10:23:31 -0500 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 h1JFNRw0027554 for ; Wed, 19 Feb 2003 09:23:28 -0600 (CST) From: "Phil Hultin" To: "Computational Chemistry List" Subject: Results (Was: Gaussian "Alter" Keyword) Date: Wed, 19 Feb 2003 09:23:29 -0600 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001B_01C2D7F8.902DFF30" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-DCC-UofM-Metrics: electra 1033; IP=ok Body=1 Fuz1=1 Fuz2=1 This is a multi-part message in MIME format. ------=_NextPart_000_001B_01C2D7F8.902DFF30 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit I was interested by the recent question about performing a calculation on a high-spin Fe(II) complex. I don't have any "technical" advice to offer as to how to get the calculation to work - that has already appeared on CCL. What caught my eye was the following: "Unfortunately the results I obtain even with the small system are hardly believable. The frontier orbitals do not resemble d orbitals very much and the spin density is not concentrated on iron (only 1/4 of it is on Fe)." The quality of the calculation may well be suspect, owing to the problems in converging, but is it really appropriate to judge the performance of a computation by how closely it reproduces the qualitative pictures we use in introducing undergraduates to electronic structure theory? In most cases that I have examined, the HOMO and LUMO do not resemble hydrogen-like atomic orbitals, nor would I expect them to. These are, after all, MOLECULAR orbital calculations. The symmetry properties of these frontier orbitals obey certain rules, but I don't know of any reason to expect them to look very much like traditional pictures of atomic orbitals. I also wonder if the fact that spin density given by the reported calculation is not concentrated where we would draw it on paper is all that significant. After all, although in organic chemistry we tend to draw methyl cation (CH3+) with the charge on carbon, calculations and other data suggest that in fact the bulk of the charge is on the hydrogens. Most experimentalists use models that are only rough approximations to reality - I include myself in that group, since I am primarily a synthetic organic chemist. But, isn't at least part of the point of doing ab initio calculations to find out more about what may be going on "under the hood" in chemical structures? What do people think about the relationship between simple qualitative models, more sophisticated ab initio models, and "reality" (whatever that may be)? 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_001B_01C2D7F8.902DFF30 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
I was = interested by=20 the recent question about performing a calculation on a high-spin Fe(II) = complex.  I don't have any "technical" advice to offer as to how to = get the=20 calculation to work - that has already appeared on CCL.  What = caught my eye=20 was the following:

"Unfortunately the results I obtain = even with=20 the small system are hardly believable. The frontier orbitals=20 do not resemble d orbitals very much and the spin density is = not=20 concentrated on iron (only 1/4 of it is on Fe)."

The quality of=20 the calculation may well be suspect, owing to the problems in = converging,=20 but is it really appropriate to judge the performance of a = computation=20 by how closely it reproduces the qualitative pictures we use = in introducing=20 undergraduates to electronic structure theory?  In most cases that = I have=20 examined, the HOMO and LUMO do not resemble hydrogen-like atomic = orbitals, nor=20 would I expect them to.  These are, after all, MOLECULAR orbital=20 calculations.  The symmetry properties of these frontier orbitals = obey=20 certain rules, but I don't know of any reason to expect them to look = very much=20 like traditional pictures of atomic orbitals.

I also wonder=20 if the fact that spin density given by the reported = calculation is not=20 concentrated where we would draw it on paper is all that = significant. =20 After all, although in organic chemistry we tend to draw methyl cation = (CH3+)=20 with the charge on carbon, calculations and other data suggest that in = fact the=20 bulk of the charge is on the hydrogens.

Most=20 experimentalists use models that are only rough approximations to = reality - I=20 include myself in that group, since I am primarily a synthetic organic=20 chemist.  But, isn't at least part of the point of doing ab initio=20 calculations to find out more about what may be going on "under the = hood" in=20 chemical structures?

What do people=20 think about the relationship between simple qualitative models, more=20 sophisticated ab initio models, and "reality" (whatever that may=20 be)?

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_001B_01C2D7F8.902DFF30-- From chemistry-request@server.ccl.net Wed Feb 19 11:07:55 2003 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1JG7sI09502 for ; Wed, 19 Feb 2003 11:07:55 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HAK0096VCT52L@mailstudenti.unimi.it> for chemistry@ccl.net; Wed, 19 Feb 2003 17:07:53 +0100 (MET) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0HAK00BGICT5K2@smtp.unimi.it> for chemistry@ccl.net; Wed, 19 Feb 2003 17:07:54 +0100 (MET) Date: Wed, 19 Feb 2003 17:12:38 +0100 From: Giulio Vistoli Subject: Re: CCL:"graphical engines" in molecular visualisation & etc. ??? To: Arturas , CCL Message-id: <002f01c2d831$b8b14e60$424f959f@farma.unimi.it> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <193412589722.20030219105241@vaidila.vdu.lt> Dear Arturas, You can use our program VEGA (http://www.ddl.unimi.it) : it is a open software to handle and visualize molecules. VEGA is a flexible environment to develop new software applications as it includes a plug in architecture (using both c++ and fortan languages) that allows to add new features to VEGA, but also to use VEGA itself as a graphical framework for specific purposes. Moreover VEGA includes a powerful visual scripting engine (based on rebol language), that allows both to automatize several operations and to modify and add new functions. Best regards Giulio Vistoli --------------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli@unimi.it http://www.ddl.unimi.it From rlw987654@netscape.net Wed Feb 19 14:05:46 2003 -0500 Return-Path: Received: from imo-r01.mx.aol.com (imo-r01.mx.aol.com [152.163.225.97]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h1JJ5kj22572 for ; Wed, 19 Feb 2003 14:05:46 -0500 (EST) Received: from rlw987654@netscape.net by imo-r01.mx.aol.com (mail_out_v34.21.) id y.10b.694223a (16237) for ; Wed, 19 Feb 2003 14:05:43 -0500 (EST) Received: from netscape.net (mow-d15.webmail.aol.com [205.188.139.131]) by air-in03.mx.aol.com (v90_r2.5) with ESMTP id MAILININ31-0219140543; Wed, 19 Feb 2003 14:05:43 -0500 Date: Wed, 19 Feb 2003 14:05:43 -0500 From: rlw987654@netscape.net To: chemistry@ccl.net Subject: Babel For Windows Message-ID: <78DC4BAB.4AA9B6F0.0347FE40@netscape.net> Hi all I just reformatted my hard drive and installed WinXP and have just finished reinstalling all my software. I'm having a problem getting Babel for Windows to work though. I have Babel 1.6 in c:\babel16\babel16 and I have Babel 1.06 in c:\babel1.06. When I try and run Babel, by clicking on Go, I get the following message in the DOS window... F:\research\TS\pna>C:\ 'C:\' is not recognized as an internal or external command, operable program or batch file. F:\research\TS\pna>cd C:\babel16\babel16 F:\research\TS\pna>babel -ipdb "F:\research\TS\pna\pnaoctamerwithadenine.pdb" -o xyz "F:\research\TS\pna\output.xyz" 'babel' is not recognized as an internal or external command, operable program or batch file. F:\research\TS\pna>pause Press any key to continue . . . Yet if I try either babel at a command prompt, it works. I also have WinXP on my desktop at home and it works fine. Please respond to me at this address with any suggestions that you may have as i am not subscribed through this address. Thanks in advance, Richard Wood, Ph. D. __________________________________________________________________ The NEW Netscape 7.0 browser is now available. Upgrade now! http://channels.netscape.com/ns/browsers/download.jsp Get your own FREE, personal Netscape Mail account today at http://webmail.netscape.com/ From chemistry-request@server.ccl.net Wed Feb 19 12:24:41 2003 Received: from gatemail.minbas.cu ([65.169.245.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1JHOaI11600 for ; Wed, 19 Feb 2003 12:24:38 -0500 Received: from mail2.minbas.cu (mail2.minbas.cu [10.16.1.3]) by gatemail.minbas.cu (Postfix) with ESMTP id 4853F810F for ; Wed, 19 Feb 2003 14:16:41 -0500 (CST) Received: from correo.minbas.cu (chab.minbas.cu [10.16.1.4]) by mail2.minbas.cu (8.11.3/8.11.3) with ESMTP id h1JHP7d60834 for ; Wed, 19 Feb 2003 12:25:07 -0500 (CST) Received: from filtermail (10.18.0.6 [10.18.0.6]) by correo.minbas.cu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id F2G8J8XW; Wed, 19 Feb 2003 12:26:13 -0500 Received: (from daemon@localhost) by filtermail (8.11.6/8.11.6) id h1JHRFZ09709 for ; Wed, 19 Feb 2003 12:27:15 -0500 Received: from UNKNOWN (10.18.0.3, claiming to be "jupiter.moa.minbas.cu") by filtermail with SMTP id smtpdrqSeqx; Wed, 19 Feb 2003 12:27:02 CST Received: from exchange.ismmm.edu.cu (172.17.0.238 [172.17.0.238]) by jupiter.moa.minbas.cu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id F2J04RWV; Wed, 19 Feb 2003 12:19:15 -0500 Received: from arenas (arenas.ismmm.edu.cu [172.16.5.52]) by exchange.ismmm.edu.cu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id 188VY4M7; Mon, 17 Feb 2003 15:46:50 -0500 Message-ID: <001e01c2d6c5$b21a61d0$340510ac@ismmm.edu.cu> From: "MSc. Alexis Otero Calvi" To: Subject: RMS Force and Maximum displacement Date: Mon, 17 Feb 2003 15:46:50 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001B_01C2D69B.C93B3210" 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_001B_01C2D69B.C93B3210 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all, We are perform the B3LYP calculation for transition metal complex with = 6-31G(d) basis set for C, H, P, S and LanL2DZ with ECP for Ni. The result: Item Value Threshold = Converged? Maximum Force 0.000003 0.000450 YES RMS Force 0.000001 0.000300 YES Maximum Displacement 0.003540 0.001800 NO=20 RMS Displacement 0.001065 0.001200 YES Predicted change in Energy=3D-2.171072D-08 Optimization completed on the basis of negligible forces. -- Stationary point found. How I can solve the problem with the RMS Force and Maximum Displacement = convergence. Alexis ------=_NextPart_000_001B_01C2D69B.C93B3210 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello all,
We are perform the B3LYP = calculation=20 for transition metal complex with 6-31G(d) basis set for C, H, P, S = and=20 LanL2DZ with ECP for Ni.
 
The result:
 
          &nbs= p;     =20 Item           &nb= sp;        =20 Value     Threshold  = Converged?
 Maximum=20 Force           &n= bsp;    =20 0.000003     0.000450    =20 YES
 RMS       =20 Force           &n= bsp;   =20  0.000001     0.000300    =20 YES
 Maximum=20 Displacement     0.003540    = ;=20 0.001800     NO=20
 RMS       =20 Displacement     0.001065    =20 0.001200     YES
 Predicted change in=20 Energy=3D-2.171072D-08
 Optimization completed on the basis of = negligible=20 forces.
    -- Stationary point = found.
How I can solve the problem with the = RMS Force and=20 Maximum Displacement convergence.
 
Alexis
 
 
 
 
 
------=_NextPart_000_001B_01C2D69B.C93B3210-- From chemistry-request@server.ccl.net Wed Feb 19 19:53:51 2003 Received: from prserv.net ([32.97.166.52]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1K0rpI18322 for ; Wed, 19 Feb 2003 19:53:51 -0500 Received: from attglobal.net (dhcp065-029-080-040.indy.rr.com[65.29.80.40]) by prserv.net (asmtp2) with SMTP id <2003022000534725200c4s3ae> (Authid: jmmckel); Thu, 20 Feb 2003 00:53:47 +0000 Message-ID: <3E53E25B.3714F83F@attglobal.net> Date: Wed, 19 Feb 2003 20:00:27 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: MPI on an NT cluster Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Folks, I have a small NT/W2K cluster of single processor machines on a 10/100 network with a fast switch. I would like to do iteratively 100's of INDO [fortran] calculations in one big job that is basically a parameter massager. I want one machine to send the same set of parameters to all "slave" nodes and to gather some computed results back to the host in order to determine the next set of parameters to be sent out to the slaves, etc, till the host decides self consistency. INDO molecular data sets could be stored on the "slaves" before hand. I am using the Digital FTN compiler that has a bunch of unix look-alikes, such as getarg, sleep, etc. If anyone has any related simple examples that I could clone, I would be most appreciative. I say this because my knowledge of MPI is trivial at best. Many thanks! John McKelvey From chemistry-request@server.ccl.net Wed Feb 19 20:08:28 2003 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1K18SI18584 for ; Wed, 19 Feb 2003 20:08:28 -0500 Received: from localhost (bushnell@localhost) by ultra.chem.ucsb.edu (8.12.3/8.12.3) with ESMTP id h1K18Dgj029147; Wed, 19 Feb 2003 17:08:15 -0800 (PST) Date: Wed, 19 Feb 2003 17:08:12 -0800 (PST) From: John Bushnell To: "MSc. Alexis Otero Calvi" cc: chemistry@ccl.net Subject: Re: CCL:RMS Force and Maximum displacement In-Reply-To: <001e01c2d6c5$b21a61d0$340510ac@ismmm.edu.cu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-milter (http://amavis.org/) The convergence criteria for forces and displacements are somewhat arbitrary, so I wouldn't characterize your output as a "problem". The forces are indeed very tiny. If you want to be sure that you have really found a good minimum, run a frequency calculation. - John On Mon, 17 Feb 2003, MSc. Alexis Otero Calvi wrote: > Hello all, We are perform the B3LYP calculation for transition metal > complex with 6-31G(d) basis set for C, H, P, S and LanL2DZ with ECP > for Ni. > > The result: > > Item Value Threshold Converged? > Maximum Force 0.000003 0.000450 YES > RMS Force 0.000001 0.000300 YES > Maximum Displacement 0.003540 0.001800 NO > RMS Displacement 0.001065 0.001200 YES > Predicted change in Energy=-2.171072D-08 > Optimization completed on the basis of negligible forces. > -- Stationary point found. > > How I can solve the problem with the RMS Force and Maximum > Displacement convergence. > > Alexis From chemistry-request@server.ccl.net Wed Feb 19 20:37:06 2003 Received: from prserv.net ([32.97.166.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1K1b6I19641 for ; Wed, 19 Feb 2003 20:37:06 -0500 Received: from attglobal.net (dhcp065-029-080-040.indy.rr.com[65.29.80.40]) by prserv.net (asmtp1) with SMTP id <2003022001370125100brgqpe> (Authid: jmmckel); Thu, 20 Feb 2003 01:37:01 +0000 Message-ID: <3E53EC79.99B0571B@attglobal.net> Date: Wed, 19 Feb 2003 20:43:37 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: John Bushnell CC: "MSc. Alexis Otero Calvi" , chemistry@ccl.net Subject: Re: CCL:RMS Force and Maximum displacement References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I agree with the below in the greatest part. The one thing I pay the most attention is the Maximum Displacement which, in my opinion, relates directly to what we really mean by getting dE/dQ arbitrarily small. This becomes especially critical when d^2E/dQ^2 might be small. I agree about a frequency check, if it is felt necessary. John McKelvey John Bushnell wrote: > The convergence criteria for forces and displacements are somewhat > arbitrary, so I wouldn't characterize your output as a "problem". > The forces are indeed very tiny. If you want to be sure that you > have really found a good minimum, run a frequency calculation. > > - John > > On Mon, 17 Feb 2003, MSc. Alexis Otero Calvi wrote: > > > Hello all, We are perform the B3LYP calculation for transition metal > > complex with 6-31G(d) basis set for C, H, P, S and LanL2DZ with ECP > > for Ni. > > > > The result: > > > > Item Value Threshold Converged? > > Maximum Force 0.000003 0.000450 YES > > RMS Force 0.000001 0.000300 YES > > Maximum Displacement 0.003540 0.001800 NO > > RMS Displacement 0.001065 0.001200 YES > > Predicted change in Energy=-2.171072D-08 > > Optimization completed on the basis of negligible forces. > > -- Stationary point found. > > > > How I can solve the problem with the RMS Force and Maximum > > Displacement convergence. > > > > Alexis > > -= 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 Wed Feb 19 21:12:35 2003 Received: from mxout1.cac.washington.edu ([140.142.32.134]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1K2CZI20848 for ; Wed, 19 Feb 2003 21:12:35 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout1.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.12) with ESMTP id h1K2COJA020001 for ; Wed, 19 Feb 2003 18:12:24 -0800 Received: from DGVR6B21 ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW01.12/8.12.1+UW02.12) with SMTP id h1K2COFj007910 for ; Wed, 19 Feb 2003 18:12:24 -0800 Message-ID: <003101c2d885$8162a1d0$74805f80@DGVR6B21> From: "Carsten Detering" To: Subject: autogrid/-dock atom types Date: Thu, 20 Feb 2003 03:12:23 +0100 Organization: University of Washington MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_002E_01C2D88D.E32275F0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 This is a multi-part message in MIME format. ------=_NextPart_000_002E_01C2D88D.E32275F0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I have a question concerning the atom types for the macro molecule in = autogrid: Usually, the types (in the autocomm.h and gpf3gen.awk files) should be = CNOSHXM (as mentioned in the autodock user's manual). Since I am working = with RNA, I removed S and X in both the autocomm.h and gpf3gen.awk files = (under #define ATOMTYPE and PROTEIN_ATOMTYPES, respectively). THis, = however, had a significant change on my calculated free energy (epdb = ligand.out.pdbq). Also, in the resulting .glg file, S and X, as well as = I are still present, although I do not have such atoms in my = macromolecules. Could kindly someone point out to me why these atom = types are still present in the log file, although I don't need them? Thanks for every comment, Carsten ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Fon 206-543-5081 Fax 206-865-8665 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------=_NextPart_000_002E_01C2D88D.E32275F0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
 
I have a question concerning the atom = types for the=20 macro molecule in autogrid:
Usually, the types (in the autocomm.h = and=20 gpf3gen.awk files) should be CNOSHXM (as mentioned in the autodock = user's=20 manual). Since I am working with RNA, I removed S and X in both the = autocomm.h=20 and gpf3gen.awk files (under #define ATOMTYPE and PROTEIN_ATOMTYPES,=20 respectively). THis, however, had a significant change on my calculated = free=20 energy (epdb ligand.out.pdbq). Also, in the resulting .glg file, S and = X, as=20 well as I are still present, although I do not have such = atoms in my=20 macromolecules. Could kindly someone point out to me why these atom = types are=20 still present in the log file, although I don't need them?
Thanks for every comment,
 
Carsten
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten = Detering,=20 Ph.D.
University of Washington
Seattle, WA 98195
Fon=20 206-543-5081
Fax=20 206-865-8665
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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