From chemistry-request@ccl.net Mon Jun 20 04:24:39 2005 Received: from nsuncom2.rz.hu-berlin.de (nsuncom2.rz.hu-berlin.de [141.20.1.28]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5K8OWFN014985 for ; Mon, 20 Jun 2005 04:24:33 -0400 Received: from localhost (suncom3.cms.hu-berlin.de [141.20.1.71]) by nsuncom2.rz.hu-berlin.de (8.12.11/8.12.11) with ESMTP id j5K8OV8T018775 for ; Mon, 20 Jun 2005 10:24:31 +0200 (MEST) Received: from suncom3.cms.hu-berlin.de ([127.0.0.1]) by localhost (suncom3 [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 04022-21-3 for ; Mon, 20 Jun 2005 10:24:28 +0200 (CEST) Received: from impact1.chemie.hu-berlin.de (impact1.chemie.hu-berlin.de [141.20.72.25]) by suncom3.cms.hu-berlin.de (8.13.1/8.13.1) with ESMTP id j5K8O3An005405 for ; Mon, 20 Jun 2005 10:24:03 +0200 (CEST) Received: from impact1.chemie.hu-berlin.de (localhost [127.0.0.1]) by impact1.chemie.hu-berlin.de (SGI-8.12.5/8.12.5) with ESMTP id j5K8O3hR257850 for ; Mon, 20 Jun 2005 10:24:03 +0200 (MESZ) Received: (from ah@localhost) by impact1.chemie.hu-berlin.de (SGI-8.12.5/8.12.5/Submit) id j5K8O2Kd279490 for chemistry #%# ccl.net; Mon, 20 Jun 2005 10:24:02 +0200 (MESZ) Date: Mon, 20 Jun 2005 10:24:02 +0200 From: "Dr. Alexander Hofmann" To: chemistry #%# ccl.net Subject: Re: CCL:CRYSTAL03 - Message-ID: <20050620082402.GB166999 #%# chemie.hu-berlin.de> Reply-To: ah #%# chemie.hu-berlin.de References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.4i X-Virus-Scanned: by amavisd-new at cms.hu-berlin.de X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello, > What now bothers me about the present structure is that using a > visualisation package I see something not resembling crystal at all! I've tried to setup the monoclinic crystal with Cerius2. It does not look like a crystal. So I think that either positions or spacegroup or both is wrong. I'd suggest to check a database or the original work for that. > Reasons why the geometry inputs cannot be wrong are: (i) I've used > different sets of well documented theoretical and experimental > geometrical inputs with the same result (ii) other geometries for other > different structures, other space groups, are very much perfect and > gives me the right crystals. > My guess is (i) there is a bug in the crystal03 code as pertains to > space group 11, but I've been assured that crystal03 code space group is > bugfree (ii) maybe the structure(Na3AlH6) was assigned the wrong space > group. Hm, may be, but as long crystal _and_ cerius2 gives the same (wrong) answer I'd like to search the error on the input side. Do you have a publication which gives _all_ positions of the atoms in the cell? Including the one generated by symmetry? This may help us. Alex -- Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie Arbeitsgruppe Quantenchemie Post: Unter den Linden 6 10099 Berlin Visitors: Brook-Taylor-Strasse 2 12489 Berlin ah #%# chemie.hu-berlin.de Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35 From chemistry-request@ccl.net Mon Jun 20 07:32:57 2005 Received: from jeeves.ccdc.cam.ac.uk (jeeves.ccdc.cam.ac.uk [131.111.113.44]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5KBWqNI023410 for ; Mon, 20 Jun 2005 07:32:53 -0400 Received: from bashful.ccdc.cam.ac.uk ([131.111.113.193] helo=ccdc.cam.ac.uk) by jeeves.ccdc.cam.ac.uk with esmtp (Exim 4.50) id 1DkJnH-0000iB-0G; Mon, 20 Jun 2005 11:46:19 +0100 Message-ID: <42B69E7A.6020806/at/ccdc.cam.ac.uk> Date: Mon, 20 Jun 2005 11:46:18 +0100 From: Jacco van de Streek Organization: CCDC User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry/at/ccl.net CC: teoricach/at/unito.it Subject: Re: CCL:CRYSTAL03 - References: In-Reply-To: Content-Type: multipart/mixed; boundary="------------050408010301010202030003" X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. --------------050408010301010202030003 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit (The short answer is: you input the incorrect space group. Both the published Na3AlH6 crystal structure and the CRYSTAL03 program are fine. See below for the long answer.) Ojwang, J.G.O. wrote: > The geometry I used are as follows: > > (a =5.33, b=5.53, c=7.68, beta=90.103)(space group(P21/n) 11) Space-group number 11 is P21/m, not P21/n. Or, to put it the opposite way round, P21/n is space-group number 14, not space-group number 11. > Al 0.0 0.0 0.0 > Na 0.0 0.0 0.5 > H 0.9897 0.4532 0.2535 > H 0.2281 0.3307 0.5437 > H 0.1608 0.2673 0.9366 In both P21/m and P21/n Al and Na with these coordinates would be on a special position with a multiplicity of 2. It is therefore not possible that these coordinates ever generate a stoichiometry of Na3AlH6: you're at least one sodium atom (not in a special position) short. I took the coordinates from the attachment called ccl2.in by Dr Alexander Hofmann. If I combine his coordinates with the symmetry operators for P21/n (space-group number 14, unique axis b, cell choice 2) I get a crystal structure that does not have any close contacts / short bonds, that has the correct soichiometry and in which the aluminum (and sodium) is symmetrically coordinated by six hydrogens. I have attached a .res file. This file format has the advantage that it only allows you to specify the symmetry operators explicitly (albeit in condensed form). You can view this crystal structure in various programs, in our freely available visualiser Mercury (available for a variety of platforms) for example: http://www.ccdc.cam.ac.uk/products/csd_system/mercury/ Mercury can also write out the file in other formats, like .mol2, and it can display the full list of symmetry operators. I wanted to check that the supercell structure was still the same as the P41/a structure by comparing the simulated powder difraction patterns, but as far as I can tell the P41/a structure in Alexander Hofmann's second attachment is missing a sodium atom again, and some hydrogens this time. If you have the P41/a structure, you can simulate the powder diffraction patterns yourself using Mercury. Best wishes, -- Dr Jacco van de Streek Research Scientist Cambridge Crystallographic Data Centre Cambridge, United Kingdom --------------050408010301010202030003 Content-Type: text/plain; name="Na3AlH6_P21n.res" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="Na3AlH6_P21n.res" TITL CCL CELL 0.71073 5.33 5.53 7.68 90 90.103 90 ZERR 4 0.000 0.000 0.000 0 0.000 0 LATT 1 SYMM 1/2-x,1/2+y,1/2-z SFAC H Na Al UNIT 12 6 2 FVAR 1.00 Al 3 0.000000 0.000000 0.000000 0.500000 0.05 Na 2 0.000000 0.000000 0.500000 0.500000 0.05 H1 1 0.100000 0.048100 0.216400 1.000000 0.05 H2 1 0.228100 0.330700 0.543700 1.000000 0.05 Na 2 -0.010300 0.453200 0.253500 1.000000 0.05 H3 1 0.160800 0.267300 -0.063400 1.000000 0.05 END --------------050408010301010202030003-- From chemistry-request@ccl.net Mon Jun 20 05:33:18 2005 Received: from mserv6.dl.ac.uk (mail.dl.ac.uk [148.79.80.137]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5K9XBhR017858 for ; Mon, 20 Jun 2005 05:33:12 -0400 X-DL-MFrom: X-DL-Connect: Received: from exchange10.dl.ac.uk (exchange10.dl.ac.uk [148.79.163.40]) by mserv6.dl.ac.uk (8.12.10/8.12.8/[ref postmaster/at/dl.ac.uk]) with ESMTP id j5K9TIPu026534 for ; Mon, 20 Jun 2005 10:32:55 +0100 Importance: normal Priority: normal Received: from exchange02.dl.ac.uk ([148.79.80.19]) by exchange10.dl.ac.uk with Microsoft SMTPSVC(6.0.3790.0); Mon, 20 Jun 2005 10:17:59 +0100 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.3790.181 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: CRYSTAL03 - Date: Mon, 20 Jun 2005 10:17:59 +0100 Message-ID: <77673C9ECE12AB4791B5AC0A7BF40C8F400D10/at/exchange02.fed.cclrc.ac.uk> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CRYSTAL03 - thread-index: AcVzY0Z1DM30+Sa5QdW/mxt0fGa4FgCFLiZg From: "Van Dam, HJJ \(Huub\)" To: Cc: "Searle, BG \(Barry\)" X-OriginalArrivalTime: 20 Jun 2005 09:17:59.0643 (UTC) FILETIME=[F3C81AB0:01C57578] X-CCLRC-SPAM-report: 0.578 : LINES_OF_YELLING,SUBJ_ALL_CAPS X-Scanned-By: MIMEDefang 2.37 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by mserv6.dl.ac.uk id j5K9TIPu026534 X-Spam-Status: No, score=0.4 required=5.0 tests=SUBJ_ALL_CAPS autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi, I have asked Barry Searle to have a look at the structure you are using. He found that the space group setting is probably not what you intended. As I am not a CRYSTAL user I don't quite understand how the input works so I have copied Barry's response below: "The user lists the Na3AlH6 space group as P21/N which is one of the settings for space group 11. The default setting for space group 11 in CRYSTAL is listed as P21/M. The CRYSTAL geometry input should be CRYSTAL 1 0 0 P 21/N 5.33 5.53 7.68 90.103 6 13 0.0 0.0 0.0 11 0.0 0.0 0.5 11 0.9897 0.4532 0.2535 1 0.1000 0.0481 0.2164 1 0.2281 0.3307 0.5437 1 0.1608 0.2673 0.9366 ENDG " I hope this solves your problem, let me know if it doesn't. Best wishes, Huub van Dam -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request/at/ccl.net]On Behalf Of Ojwang, J.G.O. Sent: 17 June 2005 17:48 To: chemistry/at/ccl.net Subject: CCL:CRYSTAL03 - Hi. I somehow sorted out the LIM007 case for a different system. The geometry was not correct! What now bothers me about the present structure is that using a visualisation package I see something not resembling crystal at all! Reasons why the geometry inputs cannot be wrong are: (i) I've used different sets of well documented theoretical and experimental geometrical inputs with the same result (ii) other geometries for other different structures, other space groups, are very much perfect and gives me the right crystals. My guess is (i) there is a bug in the crystal03 code as pertains to space group 11, but I've been assured that crystal03 code space group is bugfree (ii) maybe the structure(Na3AlH6) was assigned the wrong space group. The geometry I used are as follows: (a =5.33, b=5.53, c=7.68, beta=90.103)(space group(P21/n) 11) Al 0.0 0.0 0.0 Na 0.0 0.0 0.5 H 0.9897 0.4532 0.2535 H 0.2281 0.3307 0.5437 H 0.1608 0.2673 0.9366 I tried other different sets of geometrical inputs(experimental and theoretical) with the same results. The program calculates alright but the structure does not resemble a crystal at all. (Al should be six coordinates in H) Well, let me hear your opinion. Best Regards, Ojwang' BTW: What bothers me is (i) was the wrong space group assigned to Na3AlH6 or is there a bug in crystal03 code in so far as space group 11 is concerned. Huub van Dam email: h.j.j.vandam/at/dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603933 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD From chemistry-request@ccl.net Mon Jun 20 05:18:58 2005 Received: from ozone.few.vu.nl (ozone.few.vu.nl [130.37.20.6]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5K9ItR9017195 for ; Mon, 20 Jun 2005 05:18:55 -0400 Received: from [130.37.144.98] (europium.chem.vu.nl [130.37.144.98]) by ozone.few.vu.nl with esmtp (Smail #108) id m1DkH0c-000010C; Mon, 20 Jun 2005 09:47 +0200 Mime-Version: 1.0 (Apple Message framework v622) In-Reply-To: <755a1e3b050617142875d94e96/at/mail.gmail.com> References: <755a1e3b050617142875d94e96/at/mail.gmail.com> Content-Type: multipart/alternative; boundary=Apple-Mail-4--787448358 Message-Id: <3f0184886527b372cba080dbe98ec14f/at/few.vu.nl> From: Marcel Swart Subject: Re: CCL:Force Constants Date: Mon, 20 Jun 2005 09:47:52 +0200 To: chemistry/at/ccl.net X-Mailer: Apple Mail (2.622) X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --Apple-Mail-4--787448358 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed On Jun 17, 2005, at 11:28 PM, Pradyumna Shaakuntal Singh wrote: > Hi, > > I'm trying to compute the force constant for the superoxide ion (O2-) > using MP2/6-31G*. using Gaussian 03. The value I get after running a > frequency calculation is 11.03 mDyne/A. This converts to 68.9 eV/A^2. > The experimental value (using spectroscopic constants) is about 37.8 > eV/A^2. Clealy, I am quite off the mark. I suspect I am not > interpreting the gaussian results correctly. Could anyone throw some > light on whether I'm doign something wrong, and if so, what ? Any > help is will be appreciated. > > Thanks, > Pradyumna > > > > -=3D This is automatically added to each message by the mailing script = =3D- > To send e-mail to subscribers of CCL put the string CCL: on your =20 > Subject: line > and send your message to: CHEMISTRY/at/ccl.net > > Send your subscription/unsubscription requests to: =20 > CHEMISTRY-REQUEST/at/ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, =20 > please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-=20= > +-+ > > > > > > =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart/at/few.vu.nl Web http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-4--787448358 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 On Jun 17, 2005, at 11:28 PM, Pradyumna Shaakuntal Singh wrote: Hi, I'm trying to compute the force constant for the superoxide ion (O2-) using MP2/6-31G*. using Gaussian 03. The value I get after running a frequency calculation is 11.03 mDyne/A. This converts to 68.9 eV/A^2. The experimental value (using spectroscopic constants) is about 37.8 eV/A^2. Clealy, I am quite off the mark. I suspect I am not interpreting the gaussian results correctly. Could anyone throw some light on whether I'm doign something wrong, and if so, what ? Any help is will be appreciated. Thanks, Pradyumna -=3D This is automatically added to each message by the mailing script = =3D- 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=20 HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs=20 If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page=20 -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ = Helvetica=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96 = Papyrusdr. Marcel Swart = Papyrus = OsakaTheoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart/at/few.vu.nl Web http://www.few.vu.nl/~swart = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-4--787448358-- From chemistry-request@ccl.net Mon Jun 20 05:16:34 2005 Received: from mail.MATERIANOVA.BE (mn-vpn.materianova.be [193.190.132.26]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5K9GTWE017098 for ; Mon, 20 Jun 2005 05:16:29 -0400 Received: from mn-europe.MATERIANOVA.BE ([10.108.200.13]) by mail.MATERIANOVA.BE with Microsoft SMTPSVC(5.0.2195.6713); Mon, 20 Jun 2005 10:25:40 +0200 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: Gaussian98W memory requirements X-MimeOLE: Produced By Microsoft Exchange V6.0.6603.0 Date: Mon, 20 Jun 2005 10:25:40 +0200 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Gaussian98W memory requirements Thread-Index: AcVzgNtFcujxa5vUThyYqdqWDUvJ3wB7g9UQ From: "Igor Avilov" To: X-OriginalArrivalTime: 20 Jun 2005 08:25:40.0660 (UTC) FILETIME=[A4CD4F40:01C57571] X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5K9GYWE017105 Dear Guenther, My personal experience shows that for single-point and optimization procedures 10-15 MegaWords/80-120 MB (as set by %Mem= keyword) is sufficient for a large majority of cases. On the contrary, you would like to use all available memory for frequency/excited states calculations. Regarding your error: did you check the gaussian's default values for memory usage on your machine? Of cause, a specialist in gaussian will be able to answer your question more precisely, just looking at your error message. Did you try to ask Gaussian support team? Best regards, Igor. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request^at^ccl.net]On Behalf Of rer Sent: vendredi 17 juin 2005 21:10 To: chemistry^at^ccl.net Subject: CCL:Gaussian98W memory requirements Hello together, there are actually two questions. The first relates to an observation made by scanning the CCL archive. In almost regular time spans the question appears what to with the error codes given by Gaussian after a link dies. Surprisingly (at leat so me), a summuray of responses to these questions is apparently never posted. Does it mean that these error codes are only for the specialists > from Gaussian Inc., because no member of this list (THE experts, I suppose) has an answer to these questions so that no summary can be given? The second question relates to a hard (and unpleasant fact). A calculation is running on GAUSSIAN98W on a 3.4 GHz Pentium IV with 1 GByte working memory and 100 GByte disk space. Following the use of internal memory during a run it is found that the code never uses the internal memory to more than 20%. The calculation is a point optimisation of a lanthanide molecule with 8 water molecules (other ligand combinations were tested, the observation is the same - it seems to depend on the fact that a lanthanide ion is used). SDD pseudo cores with SDD basis sets is used for the lanthanide ion, the basis set for the light elements were successively reduced to 3-21G* (with no effect). The algorithm converges. Upon going into the next 'round', it dies with the following message: Compute integral first derivatives. Integral derivatives from FoFDir, PRISM(SPDF). Symmetry not used in FoFDir. MinBra= 0 MaxBra= 3 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Insufficient memory for a single shell combination in PrsMar called from PRISM: LenV= 57934341 MaxCom= 0 Error termination via Lnk1e in d:\gaussian98w\l703.exe. Any suggestion to get around this nasty problem is highly welcome - as is contact to other CCL members doing Gaussian calculations with lanthanides. Best regards and thanks in advance Guenther Passau, Freiberg & Toronto -= 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 is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Jun 20 11:39:24 2005 Received: from mailTM.sued-chemie.de (mailtm.sued-chemie.de [195.145.99.198]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5KFdIgG004002 for ; Mon, 20 Jun 2005 11:39:19 -0400 Received: by mailTM.sued-chemie.de (Postfix, from userid 65534) id 72FFA1A769A; Mon, 20 Jun 2005 17:41:36 +0200 (CEST) Received: from mailtm2.sued-chemie.com (unknown [172.16.1.15]) by mailTM.sued-chemie.de (Postfix) with SMTP id 8D1731A74CC for ; Mon, 20 Jun 2005 17:41:34 +0200 (CEST) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srv49003.scag.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Mon, 20 Jun 2005 17:38:40 +0200 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="GB2312" X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 Subject: RE: Force Constants Date: Mon, 20 Jun 2005 11:38:38 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0009B63F3B..at..srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Force Constants Thread-Index: AcVyvH4glacHDmj7SvWXeso8YXT+UAApVIuAAJL467A= From: "Shobe, David" To: X-OriginalArrivalTime: 20 Jun 2005 15:38:40.0126 (UTC) FILETIME=[21C539E0:01C575AE] X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net X-Spam-Level: X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5KFdOgG004009 It's been pointed out to me that the correct conversion factor is simply 6.2415. For some reason I must have interpreted "mDyne" as "&Ldyne" i.e. microdyne. --David Shobe, Ph.D., M.L.S. S(9d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request..at..ccl.net] On Behalf Of Shobe, David Sent: Friday, June 17, 2005 1:45 PM To: chemistry..at..ccl.net Subject: CCL:Force Constants 1 eV = 1.60218 x 10^-19 J thus 1 eV/A = (1.60218 x 10^-19 J)/(10^-10 m) = 1.60218 x 10^-9 N and 1 N = 6.2415 x 10^8 eV/A 1 dyne = 10^-5 N thus 1 mDyne = 10^-11 N So the conversion factor is 1 mdyne/A = 6.2415 x 10^-3 eV/A^2. --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request..at..ccl.net] On Behalf Of Pradyumna Shaakuntal Singh Sent: Thursday, June 16, 2005 12:58 PM To: chemistry..at..ccl.net Subject: CCL:Force Constants Hello, Could someone on this list please suggest how I could obtain a force-constant for a diatomic and triatomic molecule in eV/A^2 instead of mDyne/A. I am using Gaussian at the B3LYP/MP2 level. Thanks, Pradyumna -= 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 is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Jun 20 11:43:29 2005 Received: from proxy2.uh.cu (smtp2.uh.cu [200.55.139.213]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5KFhKAp004507 for ; Mon, 20 Jun 2005 11:43:23 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by proxy2.uh.cu (Postfix) with ESMTP id 1390A2FBFA for ; Mon, 20 Jun 2005 10:54:57 -0400 (CDT) Received: from fq.uh.cu (unknown [192.168.3.4]) by proxy2.uh.cu (Postfix) with ESMTP id ACFFB2FBE9 for ; Mon, 20 Jun 2005 10:54:56 -0400 (CDT) Received: from fq.uh.cu (IDENT:1565@localhost [127.0.0.1]) by fq.uh.cu (8.12.4/8.12.4/JP) with ESMTP id j5KEiNvj025258 for ; Mon, 20 Jun 2005 10:44:23 -0400 Received: from localhost (david@localhost) by fq.uh.cu (8.12.4/8.12.4/Submit) with ESMTP id j5KEiHIh025251 for ; Mon, 20 Jun 2005 10:44:23 -0400 Date: Mon, 20 Jun 2005 10:44:17 -0400 (CDT) From: David Santos Carballal To: chemistry|at|ccl.net Subject: Re: CCL:W:Molecular dynamics of silica in H2O In-Reply-To: <200506161204.j5GC4rHr006342|at|server.ccl.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by AMaViS snapshot-20020300 X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Try to use TINKER in http://dasher.wustl.edu/tinker/, you wuld download a window or linux software David Santos Carballal On Thu, 16 Jun 2005, Steven, , Kirk wrote: > Hello, > > I want to start an MD simulation of a silica particle of size 5-10 nm in aequous solution, possibly also with a few Na+ ions floating around. I have a sample PDB file containing the structure of a silica nanoparticle, and have tried to make a box containing the nanoparticle and some water molecules using the 'genbox' utility program of GROMACS. > > The problem arises when defining the parameters which determine how the atoms will interact. Does anyone have a good set of general parameters for such a system ? I am aware of the the work of Wensink and Hoffmann [Langmuir 16, 7392 (2000)], but their scheme relies on a partitioning of the system into crystal, surface and water atoms and I do not know how such a partitioning could be done in my case so as to best use their parameterization. > > I'm not 100% tied to using GROMACS (any freely available and capable MD code will do for some initial investigations). I would be grateful for any advice on alternatives. > > My investigations are intended to look into the behaviour in solution of silica nanoparticles formed by polymerization in solutions of sodium silicates, including nucleation, growth, formation of charged nanoparticles (and consequently double layers) and the effect of solution pH on this process and the detailed effects on nanoparticle surface charge density. The list above is long, I realize, but I would very much appreciate some pointers on how to get started quickly into these investigations. > > Many thanks in advance, > Steve Kirk > > > -= 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 is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Mon Jun 20 16:19:31 2005 Received: from web53304.mail.yahoo.com (web53304.mail.yahoo.com [206.190.39.233]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5KKJQnc021046 for ; Mon, 20 Jun 2005 16:19:26 -0400 Received: (qmail 38548 invoked by uid 60001); 20 Jun 2005 19:52:45 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=NsJdKmar9yKcuZeJpoi88l5A3XxiJ5GqFHVYshas5dQqlIo7QFIj9mI6fUeJZakgXThPNlw3iI0pGzFN7upF62nCfLZOUgPHfGqMAHOlRoMz97RR1RIHoAqPpdjWe0/Z+/bFBnisURynGxlxhWvR0jnsBXGNvkTvlXFnv871ByA= ; Message-ID: <20050620195245.38546.qmail/at/web53304.mail.yahoo.com> Received: from [203.200.43.195] by web53304.mail.yahoo.com via HTTP; Mon, 20 Jun 2005 12:52:45 PDT Date: Mon, 20 Jun 2005 12:52:45 -0700 (PDT) From: Chaitanya Krishna A Subject: CCL:Generating the 3D lattice from crystallographic data To: ccl MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=1.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, FROM_ENDS_IN_NUMS,RCVD_IN_NJABL_SPAM autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi all, I am a novice to crystallography. My description of the problem may not be that good. Please bear. I have the crystallographic data (cell parameters, coordinates of the asymmetric unit and the point group) about an inorganic solid (brucite) Mg(OH)2. I would like to generate the 3D lattice (say 3x3x3 unit cells) from this information and also get the xyz coordinates of all the atoms so that I can use them in my simulation. I hope I am clear on the problem. I have come across Diamond which can do this. I would like to know of the alternatives. It would be better if they run on Linux and is free. Also I have Mercury installed on my system. Is it possible to use the information that I have and use it with Mercury to generate the lattice. If yes, how can I do it? Thanks for your time. Regards, Chaitanya. ____________________________________________________ Yahoo! Sports Rekindle the Rivalries. Sign up for Fantasy Football http://football.fantasysports.yahoo.com From chemistry-request@ccl.net Mon Jun 20 15:49:38 2005 Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.194]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5KJnYqm019622 for ; Mon, 20 Jun 2005 15:49:35 -0400 Received: by wproxy.gmail.com with SMTP id 49so7182wri for ; Mon, 20 Jun 2005 12:49:34 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding:content-disposition; b=c3G64uS3ZGHZ73thzbRpNilCVJCRb52GfMHPnoLVSG92IChRREgt+lYncrFCBks1xhdRUC7IoMIDl8JoK4N4msTxC1wc6MXa3KKj6Bie3ZCatkPAQgtBDc6awO5NPePuZJfee5NEnFFf/xV1fOdt42LaUZTd1BHxKStwFwBgR3A= Received: by 10.54.59.34 with SMTP id h34mr1937wra; Mon, 20 Jun 2005 11:48:42 -0700 (PDT) Received: by 10.54.19.16 with HTTP; Mon, 20 Jun 2005 11:48:42 -0700 (PDT) Message-ID: <214e07a105062011482deafefc/at/mail.gmail.com> Date: Mon, 20 Jun 2005 14:48:42 -0400 From: Matthieu Masquelet Reply-To: Matthieu Masquelet To: chemistry/at/ccl.net Subject: CCL: Lennard-Jones parameters Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline X-Spam-Status: No, score=0.0 required=5.0 tests=RCVD_BY_IP autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5KJncqm019626 Hi everyone, First post for me here. I was wondering where I could find Lennard-Jones parameters for not so common species, such as HClO3 or different Aluminum oxides. Thanks in advance. -- Matthieu Masquelet Georgia Institute of Technology Computational Combustion Laboratory From chemistry-request@ccl.net Mon Jun 20 18:09:29 2005 Received: from sccrmhc14.comcast.net (sccrmhc14.comcast.net [204.127.202.59]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5KM9Psv027220 for ; Mon, 20 Jun 2005 18:09:25 -0400 Received: from [192.168.2.3] (c-65-97-22-208.hsd1.va.comcast.net[65.97.22.208]) by comcast.net (sccrmhc14) with SMTP id <2005062021325601400n3bvje>; Mon, 20 Jun 2005 21:32:56 +0000 Mime-Version: 1.0 (Apple Message framework v622) In-Reply-To: <20050620195245.38546.qmail = web53304.mail.yahoo.com> References: <20050620195245.38546.qmail = web53304.mail.yahoo.com> Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: <51c07511262241be4fcc65d6849fad9c = richmond.edu> From: =?ISO-8859-1?Q?Ren=E9_Kanters?= Subject: Re: CCL:Generating the 3D lattice from crystallographic data Date: Mon, 20 Jun 2005 17:32:54 -0400 To: chemistry = ccl.net X-Mailer: Apple Mail (2.622) X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5KM9Tsv027229 Hi, A long time ago (about 13 years) I wrote two small C programs that can help you with this. They are available at the CCL software repository: http://www.ccl.net/cca/software/SOURCES/C/fractional_coordinates/ index.shtml matfract allows you to generate the rest of the unit cell based on the symmetry of your space group. Note that you will have to define the matrix elements yourself. fract2xyz allows you to convert a fractional coordinate file to an xyz file. Hope this helps. Reni On Jun 20, 2005, at 3:52 PM, Chaitanya Krishna A wrote: > Hi all, > > I am a novice to crystallography. My description of the problem may not > be that good. Please bear. > > I have the crystallographic data (cell parameters, coordinates of the > asymmetric unit and the point group) about an inorganic solid (brucite) > Mg(OH)2. > > I would like to generate the 3D lattice (say 3x3x3 unit cells) from > this information and also get the xyz coordinates of all the atoms so > that I can use them in my simulation. I hope I am clear on the problem. > I have come across Diamond which can do this. I would like to know of > the alternatives. It would be better if they run on Linux and is free. > > Also I have Mercury installed on my system. Is it possible to use the > information that I have and use it with Mercury to generate the > lattice. If yes, how can I do it? > > Thanks for your time. > > Regards, > Chaitanya. > > > > ____________________________________________________ > Yahoo! Sports > Rekindle the Rivalries. Sign up for Fantasy Football > http://football.fantasysports.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 = ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST = ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, > please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > From chemistry-request@ccl.net Mon Jun 20 16:39:03 2005 Received: from web53307.mail.yahoo.com (web53307.mail.yahoo.com [206.190.39.236]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5KKd03r022302 for ; Mon, 20 Jun 2005 16:39:00 -0400 Received: (qmail 29955 invoked by uid 60001); 20 Jun 2005 19:38:59 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=AU6LpqFlJBdkAovheiV0fYv2e6cKOaYWjH4O5nftV6MzumwP7MdF6jipHrSwR/3pvbdgxdNFpLZKpFygYpeck66mf+8kUCWlB/ZwFex43BFPvi9ATvTfydeDJo9j2YJuo6c89TwAFjB+xDeMOTySlcBYSuTAT1EclvfMnSY0G4U= ; Message-ID: <20050620193859.29953.qmail = web53307.mail.yahoo.com> Received: from [203.200.43.195] by web53307.mail.yahoo.com via HTTP; Mon, 20 Jun 2005 12:38:59 PDT Date: Mon, 20 Jun 2005 12:38:59 -0700 (PDT) From: Chaitanya Krishna A Subject: CCL:Programs to compute the energies of inorganic solids To: ccl MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=1.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, FROM_ENDS_IN_NUMS,RCVD_IN_NJABL_SPAM autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi, I am planning to work on inorganic solids, specifically the double layered hydroxides. I would like to know if any programs are available to compute the energies of these systems. I would also like do some molecular dynamics simulations with these systems. I have come across DL_POLY and GULP. Are there any other similar programs or better programs which can achieve the job. Thanks for your time. Regards, Chaitanya. ____________________________________________________ Yahoo! Sports Rekindle the Rivalries. Sign up for Fantasy Football http://football.fantasysports.yahoo.com From chemistry-request@ccl.net Mon Jun 20 18:32:55 2005 Received: from jeeves.ccdc.cam.ac.uk (jeeves.ccdc.cam.ac.uk [131.111.113.44]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5KMWqM9028895 for ; Mon, 20 Jun 2005 18:32:52 -0400 Received: from localhost ([127.0.0.1] helo=jeeves.ccdc.cam.ac.uk ident=www-data) by jeeves.ccdc.cam.ac.uk with esmtp (Exim 4.50) id 1DkUGw-0004XT-Bv for chemistry..at..ccl.net; Mon, 20 Jun 2005 22:57:38 +0100 Received: from cpc2-cmbg7-3-0-cust84.cmbg.cable.ntl.com ([82.4.148.84]) (SquirrelMail authenticated user jaccos) by jeeves.ccdc.cam.ac.uk with HTTP; Mon, 20 Jun 2005 22:57:38 +0100 (BST) Message-ID: <1208.82.4.148.84.1119304658.squirrel..at..jeeves.ccdc.cam.ac.uk> In-Reply-To: <20050620195245.38546.qmail..at..web53304.mail.yahoo.com> References: <20050620195245.38546.qmail..at..web53304.mail.yahoo.com> Date: Mon, 20 Jun 2005 22:57:38 +0100 (BST) Subject: Re: CCL:Generating the 3D lattice from crystallographic data From: jaccos..at..ccdc.cam.ac.uk To: chemistry..at..ccl.net User-Agent: SquirrelMail/1.4.4 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net > I have the crystallographic data (cell parameters, coordinates of the > asymmetric unit and the point group) about an inorganic solid (brucite) > Mg(OH)2. > > I would like to generate the 3D lattice (say 3x3x3 unit cells) from > this information and also get the xyz coordinates of all the atoms so > that I can use them in my simulation. I hope I am clear on the problem. > I have come across Diamond which can do this. I would like to know of > the alternatives. It would be better if they run on Linux and is free. > > Also I have Mercury installed on my system. Is it possible to use the > information that I have and use it with Mercury to generate the > lattice. If yes, how can I do it? Yes, that is possible with Mercury. Switch on packing (the check box in the left-hand bottom cormner of the main window), then under "Calculate" from the menu bar select "Packing/Slicing...". In the dialogue that pops up, set the ranges for a, b and c all from 0.0 to 3.0. Then, from the menu bar, select "File" and "Save As...". Save your file as a PDB file (*.pdb) or as a Mol2 (*.mol2) if you want orthogonal coordinates (which I guess is what you want) or save as a Cif file (*.cif) if you want fractional coordinates. If you only require x, y, z, then that is possible by clicking on "More Info" then "Atom List...", and then to customise what is displayed in the columns by clicking "Costumise..." and adding Xorth, Yorth and Zorth while removing everything else. If you then save the spread sheet by clicking "Save...", the file will contain the orthogonal coordinates in tab separated form. Best wishes, -- Dr Jacco van de Streek Research Scientist Cambridge Crystallographic Data Centre Cambridge, United Kingdom From chemistry-request@ccl.net Mon Jun 20 20:00:24 2005 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5L00BFY001627 for ; Mon, 20 Jun 2005 20:00:18 -0400 Received: from hermes.scripps.edu (hermes [137.131.140.49]) by relay1.scripps.edu (8.12.11/TSRI-5.0.2rAV) with ESMTP id j5KNKruI020609; Mon, 20 Jun 2005 16:20:53 -0700 (PDT) Received: from [137.131.108.32] (newton [137.131.108.32]) by hermes.scripps.edu (8.12.9+Sun/TSRI-5.1AV) with ESMTP id j5KNKq1E011776; Mon, 20 Jun 2005 16:20:53 -0700 (PDT) Mime-Version: 1.0 (Apple Message framework v730) In-Reply-To: <20050618225857.40395.qmail..at..web41201.mail.yahoo.com> References: <20050618225857.40395.qmail..at..web41201.mail.yahoo.com> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: 7bit From: "Dr. Garrett M. Morris" Subject: Re: CCL:autodock3 dies upon launch with multiple errors Date: Mon, 20 Jun 2005 16:20:52 -0700 To: chemistry..at..ccl.net, Robyn Ayscue X-Mailer: Apple Mail (2.730) X-Virus-Scanned: ClamAV 0.85.1/947/Mon Jun 20 12:39:23 2005 on hermes X-Virus-Status: Clean X-CanItPRO-Stream: admin redirected to 10_OptOut X-Spam-Score: undef - spam-scanning disabled X-Scanned-By: CanIt (www . roaringpenguin . com) on 137.131.200.29 X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi Robyn, You should make sure that the path includes the directory that contains these scripts; for example: set path = ($path /full/path/to/dist305/share ) if you had installed the AutoDock distribution in "/full/path/to/ dist305". Put this command in your ".cshrc" and the next time you open a terminal window, you will have the correct path. Garrett On Jun 18, 2005, at 3:58 pm, Robyn Ayscue wrote: > Yong, > > I tried the mkdpf3 command you gave me. I end up with > this error: > > frodo 6@ > /disk02/usr/local/autodock/dist305/share/mkdpf3 > DPN_adt.out.pdbq 2c9q_HEMq_FLPq.pdbqs > > ______________________________________________________________________ > __________ > mkdpf3 > (C) 1999, Garrett Morris, TSRI. > > Ligand = "DPN_adt.out.pdbq", Macromolecule = > "2c9q_HEMq_FLPq.pdbqs". > > Making "DPN_adt.out.2c9q_HEMq_FLPq.dpf", based on the > atom types found in "DPN_adt.out.pdbq" > > >> ...Using "dpf3gen". >> > > dpf3gen - Command not found > > Sorry, I could not create > DPN_adt.out.2c9q_HEMq_FLPq.dpf > ______________________________________________________________________ > __________ > > > But I DO have dpf3gen; I did a "find -name" in the > c-shell and found it. Do you think it's just a matter > of the path for the software not being set? > > Thanks for your help! > > Robyn > > > --- Yong Liang Yang wrote: > > >> Dear Robyn: >> >> In a command window in IRIX, >> >> try, >> >> # mkdpf3 .pdbq .pdbqs >> >> this will produce a ..dpf file, then >> >> try >> >> # autodock3 -p ..dpf -l >> ..dlg& >> >> This might work if ADT could not launch the job. >> >> >> >> Cheers >> >> >> Yong >> >> >> >> >> >> >> >> >> On Fri, 17 Jun 2005, Robyn Ayscue wrote: >> >> >>> All, >>> >>> Sorry for the cross-post. >>> >>> I'm running AutoDockTools using autodock/autogrid >>> version 3.05 on an SGI machine with IRIX 6.5.24. >>> >> I'm >> >>> trying to dock an effector molecule in the active >>> >> site >> >>> of an enzyme (p450 2c9) with a substrate molecule >>> >> also >> >>> present. Autogrid finishes out with no problems, >>> >> but >> >>> autogrid dies immediately upon launch with the >>> following errors: >>> >>> >>> Can't find ".dpf" in the dock-parameter filename. >>> >>> AutoDock needs the extension of the grid parameter >>> file to be ".gpf" >>> and that of the docking parameter file to be >>> >> ".dpf". >> >>> >>> >>> >> >> > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/ > autodock3: > >>> Wrong number of x grid-points in grid-map file >>> "2c9q_HEMq_FLPq.A.map". >>> >>> >> >> > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/ > autodock3: > >>> Use either 32 or 1129013060 throughout! >>> >>> >> >> > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/ > autodock3: > >>> ERROR: Using wrong grid-map file. >>> >>> >>> >> >> > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/ > autodock3: > >>> Aborting... >>> >>> >>> >> >> > /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/ > autodock3: > >>> Unsuccessful Completion. >>> >>> >>> First it complains about not being able to find a >>> docking parameter file with .dpf as the suffix, >>> >> but >> >>> the file DOES have a .dpf suffix and it is listed >>> >> as >> >>> having one in the command that is typed in the >>> >> command >> >>> line used to launch autodock. The .dpf file looks >>> >> fine >> >>> as far as I can tell, compared to other .dpf files >>> I've used for other docking runs that have >>> >> completed >> >>> successfully. >>> >>> The next thing it complains about is the differing >>> number of grid points. It keeps referring to the >>> number "1129013060" but I can't find that number >>> >> in >> >>> any of the grid-map files. The number of x- grid >>> points in all grid-map files is the same. >>> >>> Autodock comes to the conclusion that I'm using >>> >> the >> >>> wrong grid-map files, but the files I'm using ARE >>> >> the >> >>> correct files (I checked and double-checked). >>> >>> If anyone has had experience with this kind of >>> >> error >> >>> message and knows how to resolve it, I'd >>> >> appreciate >> >>> any input. Thanks much! >>> >>> Robyn Ayscue >>> rayscue..at..hsc.wvu.edu >>> kajsicat..at..yahoo.com >>> >>> >>> >>> >>> >>> >>> >>> >> ____________________________________________________ >> >>> Yahoo! Sports >>> Rekindle the Rivalries. Sign up for Fantasy >>> >> Football >> >>> http://football.fantasysports.yahoo.com >>> >>> >>> >>> Send your subscription/unsubscription requests to: >>> >> CHEMISTRY-REQUEST..at..ccl.net >> >>> HOME Page: http://www.ccl.net | Jobs Page: >>> >> http://www.ccl.net/jobs >> >>> >>> use the Web based form from CCL Home Page >>> >>> >>> >>> >>> >>> >> >> >> -= 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 >> >> 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 is mail bouncing from ccl.net domain due to >> spam filters, please >> >> >> >> >> >> >> >> > > > > > ____________________________________________________ > Yahoo! Sports > Rekindle the Rivalries. Sign up for Fantasy Football > http://football.fantasysports.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 is mail bouncing from ccl.net domain due to spam filters, > please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > > ___ Dr Garrett M. Morris, MA, DPhil The Scripps Research Institute, tel: (858) 784-2292 Dept. Molecular Biology, MB-5, fax: (858) 784-2860 10550 North Torrey Pines Road, email: garrett..at..scripps.edu La Jolla, CA 92037-1000, USA. www.scripps.edu/mb/olson/gmm From chemistry-request@ccl.net Mon Jun 20 20:00:18 2005 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5L00BFW001627 for ; Mon, 20 Jun 2005 20:00:11 -0400 Received: from hermes.scripps.edu (hermes [137.131.140.49]) by relay1.scripps.edu (8.12.11/TSRI-5.0.2rAV) with ESMTP id j5KNUnl8021661; Mon, 20 Jun 2005 16:30:49 -0700 (PDT) Received: from [137.131.108.32] (newton [137.131.108.32]) by hermes.scripps.edu (8.12.9+Sun/TSRI-5.1AV) with ESMTP id j5KNUn1E014131; Mon, 20 Jun 2005 16:30:49 -0700 (PDT) Mime-Version: 1.0 (Apple Message framework v730) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: Cc: autodock..at..scripps.edu, chemistry..at..ccl.net Content-Transfer-Encoding: 7bit From: "Dr. Garrett M. Morris" Subject: An unreproducible error: autodock3 dies upon launch with multiple errors Date: Mon, 20 Jun 2005 16:30:49 -0700 To: Robyn Ayscue X-Mailer: Apple Mail (2.730) X-Virus-Scanned: ClamAV 0.85.1/947/Mon Jun 20 12:39:23 2005 on hermes X-Virus-Status: Clean X-CanItPRO-Stream: admin redirected to 10_OptOut X-Spam-Score: undef - spam-scanning disabled X-Scanned-By: CanIt (www . roaringpenguin . com) on 137.131.200.29 X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi Robyn, Thanks for sending me the 4 input files and the information about your SGI hardware and OS version. I tested the compiled AutoGrid and AutoDock executables we are currently distributing on one of our SGIs running the same version of IRIX as your machine, and AutoGrid computed the maps fine. When I ran AutoDock it complained that: ./dist305/src/autodock/autodock3: I'm sorry; I can't find or open "DPN_adt2.out.pdbq" ________________________________________________________________________ ________ [1] Exit 255 ./dist305/src/autodock/autodock3 -p 2c9_HEMq_FLPq.dpf -l log.dlg so I edited the DPF you sent me to look for the ligand PDBQ file you sent me (DPN_adt2.out.pdbq), and re-ran AutoDock. Everything worked fine. So I am mystified as to why you had this problem. Is is possible that you did not have any disk space and the maps have a size of 0? Did you or someone else modify the source code we sent you, and re-compile AutoDock? When did you download AutoDock--could it be you have a really old binary? Sorry I can't be more helpful, Garrett ___ Dr Garrett M. Morris, MA, DPhil The Scripps Research Institute, tel: (858) 784-2292 Dept. Molecular Biology, MB-5, fax: (858) 784-2860 10550 North Torrey Pines Road, email: garrett..at..scripps.edu La Jolla, CA 92037-1000, USA. www.scripps.edu/mb/olson/gmm