From chemistry-request@server.ccl.net Thu Apr 5 04:37:37 2001 Received: from cascara.UVic.CA (root@[142.104.5.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f358baD30445 for ; Thu, 5 Apr 2001 04:37:37 -0400 Received: from pinc233.pinc.com (pinc233.pinc.com [199.60.118.233]) by cascara.UVic.CA (8.11.2/8.11.2) with SMTP id f358aHf99322; Thu, 5 Apr 2001 01:36:17 -0700 From: Roy Jensen To: Xavier ASSFELD Cc: Chemistry@ccl.net, matz@wsunix.wsu.edu Subject: Re: CCL:symmetry change Date: Thu, 05 Apr 2001 01:37:22 -0700 Message-ID: <85boctc85is7ou8rdr0l43ode6dr68ug7c@4ax.com> References: <157A51F55AAAD3119CD70008C7B1629DDAADDE@lvlxch01.unitedcatalysts.com> <3ACB3694.A075CF73@lctn.uhp-nancy.fr> <3ACC20DF.B5289973@lctn.uhp-nancy.fr> In-Reply-To: <3ACC20DF.B5289973@lctn.uhp-nancy.fr> X-Mailer: Forte Agent 1.8/32.548 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f358bbD30446 The following simple job dies as stated. I am using G98W A.9. Phillip has a H2O input file that also fails. I am curious if his also completes a complete iteration after the symmetry change is detected before crashing with x=2. Roy Jensen ********************************************** #P UB3LYP/3-21G opt(verytight) IOP(2/9=222,2/16=3) Sample run to show problem with IOP(2/16=x) and changing symmetry. x=1,2,3 should allow the job to continue when the symmetry changes. This is not the case. A FIOCOM error occurs one or two iterations after the symmetry change is detected: x=1 or 3 dies immediately after the symmetry change is detected. x=2 completes one itteration and then dies. 0 1 H N 1 R1 C 2 R2 1 A1 X 3 1. 2 90. 1 0. O 3 R3 4 A2 1 D1 R1=1.00 R2=1.20 R3=1.19 A1=140.7 A2=86.2 D1=179.9999 ********************************************** On Thu, 05 Apr 2001 09:38:07 +0200, you wrote: > Roy Jensen wrote: > > > > I have not been able to get this IOP to work in G98W. Gaussian is > > aware of the error; I have sent them a simple input file that fails. > > No response yet... > > > > Roy Jensen > > > > > Instead of the NOSYM keyword, and loosing the efficiency..., you can use > > > the > > > keyword IOP(2/16=N) which keeps all advantages of symmetry and keep > > > going if the point group change. > > > If N=1 : keep going > > > N=2 : keep going and leave symmetry on, using the old symmetry > > > N=3 : keep going and leave symmetry on, using the new symmetry. > > Which value is not working? I use IOP(2/16=1) and it works perfectly, > at least as long as I remember. Could you, please, send me the input > file which presents this discrepancy. I am very curious about it. > Yours. From chemistry-request@server.ccl.net Thu Apr 5 05:47:39 2001 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f359lcD30927 for ; Thu, 5 Apr 2001 05:47:38 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.11.2/8.11.2/Guy-12-01-2001) with ESMTP id f359lah06048; Thu, 5 Apr 2001 11:47:37 +0200 (METDST) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id LAA22420; Thu, 5 Apr 2001 11:48:42 +0200 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3ACC3DA7.17193100@lctn.uhp-nancy.fr> Date: Thu, 05 Apr 2001 11:40:55 +0200 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: Roy Jensen , CCL Subject: Re: CCL:symmetry change References: <157A51F55AAAD3119CD70008C7B1629DDAADDE@lvlxch01.unitedcatalysts.com> <3ACB3694.A075CF73@lctn.uhp-nancy.fr> <3ACC20DF.B5289973@lctn.uhp-nancy.fr> <85boctc85is7ou8rdr0l43ode6dr68ug7c@4ax.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Amazing! I tried, unsuccessfuly, to make your job run correctly. You are right. This keyword fails when the symmetry is increased. In all the cases I have studied so far, the symmetry was decreased and the keyword seems to work fine. here follows a small example. # HF/STO-3G SCF=DIRECT SCAN IOP(2/16=3) NH3 0 1 X N 1 1. H 2 R 1 A H 2 R 1 A 3 120. H 2 R 1 A 3 240. R 0.9 A 90. 3 10. -- ...Xav WARNING! NEW E-MAIL ADDRESS ! (u-nancy changed to uhp-nancy) Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Thu Apr 5 08:03:13 2001 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f35C3DD00940 for ; Thu, 5 Apr 2001 08:03:13 -0400 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) with ESMTP id PAA17781 for ; Thu, 5 Apr 2001 15:21:27 +0200 (CEST) Date: Thu, 5 Apr 2001 15:21:27 +0200 From: Christian Pilger To: chemistry@ccl.net Subject: structure verification In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I ran a series of MD calculations on a protein, partially solvated in water with the aim to equilibrate the solvent molecules. The equilibrated structure is going to be employed in a docking study. I would like to ask for your opinions: is it valuable/necessary to check such an equilibrated protein structure by means of tools available for structure verification in macromulecular Xray crystalography/NMR spectroscopy, such as WHATIF and/or ADIT from the PDB ? Are there other programs available for this type of validation ? Ciao, Christian ----------------------------------------------------------------- Dr. Christian Pilger Istituto di Strutturistica Chimica "Giordano Giacomello" C.N.R. - Sezione di Trieste Area Science Park - Basovizza Strada Statale 14 - Km. 163.5 I-34012 Trieste/Italy Tel.: +39+040+226881 Fax : +39+040+9221126 e-mail: cpilger@oc30.uni-paderborn.de ----------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Apr 5 08:19:52 2001 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f35CJoD01086 for ; Thu, 5 Apr 2001 08:19:50 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.11.2/8.11.2/Guy-12-01-2001) with ESMTP id f35CJkV05422; Thu, 5 Apr 2001 14:19:46 +0200 (METDST) Received: from host5 (host5.lctn.uhp-nancy.fr [193.50.239.5]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with SMTP id OAA25528; Thu, 5 Apr 2001 14:20:51 +0200 Content-Type: text/plain; charset="ISO 8859-1" From: Nicolas Ferre Organization: Laboratoire de Chimie Theorique de Nancy To: Roy Jensen , Xavier ASSFELD Subject: Re: CCL:symmetry change Date: Thu, 5 Apr 2001 13:12:46 +0100 X-Mailer: KMail [version 1.2] Cc: Chemistry@ccl.net, matz@wsunix.wsu.edu References: <157A51F55AAAD3119CD70008C7B1629DDAADDE@lvlxch01.unitedcatalysts.com> <3ACC20DF.B5289973@lctn.uhp-nancy.fr> <85boctc85is7ou8rdr0l43ode6dr68ug7c@4ax.com> In-Reply-To: <85boctc85is7ou8rdr0l43ode6dr68ug7c@4ax.com> MIME-Version: 1.0 Message-Id: <01040514124602.03306@host5> Content-Transfer-Encoding: 8bit Hi all, In fact, it is a read-write file error. Due to the symmetry increase, the amount of memory allocated for this rwf (579) is not sufficient. To correct this bug, if you have access to the source code, you can add the following lines in the link 202. In subroutine Omega, just before the line Call FileIO(1,-IRwNEq,InToWP(NOp2*NAtoms),NEqAtm,0) add CALL FILEIO(11,-IRWNEQ,LEN,NEqAtm,0) IF(LEN.NE.0) THEN LEN=INTOWP(NOP2*NATOMS)-LEN CALL FILEIO(20,-IRWNEQ,LEN,NEqAtm,0) ENDIF It adjusts the length of the rwf. The job you gave now works fine ... until it crashes because 20 optimization steps are not enough to achieve a verytight optimization job ! Nicolas On Thursday 05 April 2001 10:37, Roy Jensen wrote: > The following simple job dies as stated. I am using G98W A.9. > Phillip has a H2O input file that also fails. I am curious if his also > completes a complete iteration after the symmetry change is detected > before crashing with x=2. > > Roy Jensen > > ********************************************** > #P UB3LYP/3-21G opt(verytight) IOP(2/9=222,2/16=3) > > Sample run to show problem with IOP(2/16=x) and changing symmetry. > x=1,2,3 should allow the job to continue when the symmetry changes. > This is not the case. A FIOCOM error occurs one or two iterations > after the symmetry change is detected: > x=1 or 3 dies immediately after the symmetry change is detected. > x=2 completes one itteration and then dies. > > 0 1 > H > N 1 R1 > C 2 R2 1 A1 > X 3 1. 2 90. 1 0. > O 3 R3 4 A2 1 D1 > > R1=1.00 > R2=1.20 > R3=1.19 > A1=140.7 > A2=86.2 > D1=179.9999 > ********************************************** > > On Thu, 05 Apr 2001 09:38:07 +0200, you wrote: > > Roy Jensen wrote: > > > I have not been able to get this IOP to work in G98W. Gaussian is > > > aware of the error; I have sent them a simple input file that fails. > > > No response yet... > > > > > > Roy Jensen > > > > > > > Instead of the NOSYM keyword, and loosing the efficiency..., you can > > > > use the > > > > keyword IOP(2/16=N) which keeps all advantages of symmetry and keep > > > > going if the point group change. > > > > If N=1 : keep going > > > > N=2 : keep going and leave symmetry on, using the old symmetry > > > > N=3 : keep going and leave symmetry on, using the new symmetry. > > > > Which value is not working? I use IOP(2/16=1) and it works perfectly, > > at least as long as I remember. Could you, please, send me the input > > file which presents this discrepancy. I am very curious about it. > > Yours. > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net -- Nicolas FERRE Equipe de Chimie Theorique - UMR UHP/CNRS 7565 BP 139 - 54506 VANDOEUVRE-LES-NANCY - FRANCE Phone: +33 3 83 91 20 00 (ask for 35 52) Fax : +33 3 83 91 25 30 http://www.lctn.uhp-nancy.fr/Etudiants/Nicolas.Ferre.html From chemistry-request@server.ccl.net Thu Apr 5 03:55:29 2001 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f357tRD30126 for ; Thu, 5 Apr 2001 03:55:28 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.11.2/8.11.2/Guy-12-01-2001) with ESMTP id f357tQB11108; Thu, 5 Apr 2001 09:55:26 +0200 (METDST) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id JAA26058; Thu, 5 Apr 2001 09:56:31 +0200 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3ACC235C.7B0C9C63@lctn.uhp-nancy.fr> Date: Thu, 05 Apr 2001 09:48:44 +0200 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: "Phillip D. Matz" CC: Bernd Schubert , Chemistry Subject: Re: CCL:symmetry change References: <01040423430701.00680@bathl> <000d01c0bd5c$c78be950$b4297986@chem.wsu.edu> Content-Type: multipart/mixed; boundary="------------BFB9AD75AEA61A0B08BD7102" This is a multi-part message in MIME format. --------------BFB9AD75AEA61A0B08BD7102 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit [jkl@ccl.net -- sorry but I had to zip the attachment to shrink to manageable size (from over 60k to about 13k)] "Phillip D. Matz" wrote: > > Hi, > > In G98W A.7 (SCAN job changing Cs to C2v to Cs for H2O): > IOP(2/16=3) -> crashes on "Operation on file out of range." > IOP(2/16=2) -> crashes on "Error in generated initial guess." > IOP(2/16=1) -> crashes on "Operation on file out of range." > > In G98 A.7 (SCAN job changing Cs to C2v to Cs for H2O): > IOP(2/16=3) -> crashes on "Operation on file out of range." > IOP(2/16=2) -> crashes on "Error in generated initial guess." > IOP(2/16=1) -> crashes on "Operation on file out of range." > > It does not appear to matter with rev A.7 whether you employ the windows > version or the linux version of G98, the generated errors are identical. I > guess we're stuck with the nosymm option... > > Respectfully, > > Phillip Matz > matz@wsunix.wsu.edu > Here are attached output files from G98.A7 with the various keywords. All of them work perfectly! ...Xav WARNING! NEW E-MAIL ADDRESS ! (u-nancy changed to uhp-nancy) Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr --------------BFB9AD75AEA61A0B08BD7102 Content-Type: APPLICATION/ZIP; name="h2o.zip" Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: compressed h2o.iop1 gaussian output Content-Disposition: attachment; filename="h2o.zip" UEsDBBQAAAAIAFdOhSoTOfsfsx0AAMT7AAAIAAAAaDJvLmlvcDHsXFt32ziS ftevwOl9aLtXpAnwnl7tWdnyLYktj+QkTkbzQEuwxLFEakjKifrX71cgJVEX X9JRutOnheMLCaIKVYVCoQoEix1HmUzCqM9Og0mahkHE2tM0k6MqextG98yo HXwW5kHf9+i3ws6jMAuDIevGo1EQ9V5V2Pz5kOvyi2QHKe5vgodQJlTNPYdb B0CucdcwhR5GY6al3aQXJrWNTStsTpKigLPaWh9X540ao8Jt23X0CmMVdhSP p0nYH2Rsr7vPuO95Ve77Bv0R9MekPzb98ea8VsFPl8BXS304ZC1ClrKWTGXy IHt5L9eDMGX4GQdJxuI7lg3kHNtea58B+TiJ+0kw0hk7z6jpbZDKHoujylJj 5lt71xf7LFXSBs1z8onMFQr3q6vA4nFg8Syw8Tiw8Ryw5z0K7HnPAjuPAzvs KEgi2Q8lu5DDIcnrXRQ+yCQNs+l+lUHbVpA9LgPPrKxiKyPTF0gwPgG7kz2Z 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ghsPrQ4e4OI90nQk34tMK1P5ImTaZILN628Nom5EBksQ+vN/UEsBAhMDFAAA AAgAV06FKhM5+x+zHQAAxPsAAAgAAAAAAAAAAQAAAKSBAAAAAGgyby5pb3Ax UEsFBgAAAAABAAEANgAAANkdAAAAAA== --------------BFB9AD75AEA61A0B08BD7102-- From chemistry-request@server.ccl.net Thu Apr 5 05:23:34 2001 Received: from localhost.localdomain ([141.250.13.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f359NXD30794 for ; Thu, 5 Apr 2001 05:23:34 -0400 Received: (from mirco@localhost) by localhost.localdomain (8.11.0/8.11.0) id f359Jmf00906 for chemistry@ccl.net; Thu, 5 Apr 2001 11:19:48 +0200 Date: Thu, 5 Apr 2001 11:19:48 +0200 From: Mirco Meniconi <> To: chemistry@ccl.net Subject: interation energy between molecule and probe Message-ID: <20010405111948.A728@cost> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i Hi all, I need to calculate with semiempirical or ab initio methods the interaction energy between a molecule and an array of probes ( like O, H2O, NH3 ecc.). with which software can I do this? thanks From chemistry-request@server.ccl.net Thu Apr 5 11:03:31 2001 Received: from po.cwru.edu (root@[129.22.4.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f35F3VD02393 for ; Thu, 5 Apr 2001 11:03:31 -0400 Received: from gavin (chem51286.CHEM.CWRU.Edu [129.22.129.217]) by po.cwru.edu with SMTP (8.8.8+cwru/CWRU-3.6) id LAA12674; Thu, 5 Apr 2001 11:02:13 -0400 (EDT) (from hxt10@po.cwru.edu) Message-ID: <007701c0bde1$f80d8220$d9811681@cwru.edu> Reply-To: "Hui-Hsu \(Gavin\) Tsai" From: "Hui-Hsu \(Gavin\) Tsai" To: "Xavier ASSFELD" Cc: References: <01040423430701.00680@bathl> <000d01c0bd5c$c78be950$b4297986@chem.wsu.edu> <3ACC235C.7B0C9C63@lctn.uhp-nancy.fr> Subject: Re: CCL:symmetry change Date: Thu, 5 Apr 2001 11:06:19 -0400 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 By inspecting the outfile, I find something different... for IOP(2/16=1) option, the symmetry is turned off "Omega -- symmetry turned off." for IOP(2/16=2) option, the job is terminated "Error in generated initial guess. Error termination via Lnk1e in /w23/g98/l401.exe." For IOP(2/16=3) option, job is finished, but I will suggest you to use #P option to print out more information at every iteration. The density matric maybe broken. My points are we probably did not take any advantage of this option because symmetry is either turned off or broken Gavin ----- Original Message ----- From: "Xavier ASSFELD" To: "Phillip D. Matz" Cc: "Bernd Schubert" ; "Chemistry" Sent: Thursday, April 05, 2001 3:48 AM Subject: CCL:symmetry change > [jkl@ccl.net -- sorry but I had to zip the attachment to shrink > to manageable size (from over 60k to about 13k)] > > "Phillip D. Matz" wrote: > > > > Hi, > > > > In G98W A.7 (SCAN job changing Cs to C2v to Cs for H2O): > > IOP(2/16=3) -> crashes on "Operation on file out of range." > > IOP(2/16=2) -> crashes on "Error in generated initial guess." > > IOP(2/16=1) -> crashes on "Operation on file out of range." > > > > In G98 A.7 (SCAN job changing Cs to C2v to Cs for H2O): > > IOP(2/16=3) -> crashes on "Operation on file out of range." > > IOP(2/16=2) -> crashes on "Error in generated initial guess." > > IOP(2/16=1) -> crashes on "Operation on file out of range." > > > > It does not appear to matter with rev A.7 whether you employ the windows > > version or the linux version of G98, the generated errors are identical. I > > guess we're stuck with the nosymm option... > > > > Respectfully, > > > > Phillip Matz > > matz@wsunix.wsu.edu > > > > Here are attached output files from G98.A7 with the various keywords. > All of them work perfectly! > > ...Xav > > WARNING! NEW E-MAIL ADDRESS ! > (u-nancy changed to uhp-nancy) > > Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr > Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 > Universite Henri Poincare (F) 33 3 83 91 25 30 > F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Thu Apr 5 10:19:22 2001 Received: from gatekeeper.itqb.unl.pt (qmailr@[193.136.177.1]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f35EJLD02103 for ; Thu, 5 Apr 2001 10:19:21 -0400 Received: (qmail 29217 invoked from network); 5 Apr 2001 14:19:17 -0000 Received: from mistral.itqb.unl.pt (sgodinho@193.136.176.14) by gatekeeper.itqb.unl.pt with SMTP; 5 Apr 2001 14:19:17 -0000 Received: from localhost (sgodinho@localhost) by mistral.itqb.unl.pt (8.9.3/8.9.3) with ESMTP id PAA23799 for ; Thu, 5 Apr 2001 15:19:17 +0100 Date: Thu, 5 Apr 2001 15:19:16 +0100 (WEST) From: Sofia Godinho To: CCL Subject: summary: charge in a point outside a molecule Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I thank all the people who have tried to help me. Summary of the answers order by date of arrival obtained to the following message: * Dear CCLers, * I wonder if anyone can teach me how to calculate, with Gaussian, the * charge in a specific point of the space outside a molecule. Let's say * in a point defined by x,y,z coordinates away from that molecule. * Thank you in advance for your help, * Sofia Godinho ----------------------------------------------------------------------- From: Alexander Wittkopp Hi, I don't think you can place a charge somewhere in space, but since elektrones can only be where basis sets are you just have to define an origin for those and set the over all charge to -1, or whatever you like. E.g. you could place a helium atom where you want to place your charge and set the Nuc.-charge of He to 0 (keyword: massage). With Gen you can modify the shape of this charge, by modifying the basis set of He. This procedure does not guarantee that your overall charge lands on this 'ghost basis set', it will be distributed all along the whole molecule but it is the only method I can think of. This method has been used to determine the 'stability' of solvated electrons. (I think T. Clark, end of the 80s) Cheers, Alexander PS: Let me know if somebody has nicer ideas! -------------------------------------------------------------------------- From: "Shobe, Dave" Your question is open to interpretation: If you mean to calculate the "charge" at a point in space, which is caused by the electron density and electric field of the molecule, the answer is zero (or "infinitesimal" if you like). However, there is such a thing as the charge *density* at a point, which is (in absolute values anyway) the same as the electron density, and which *integrated over a region* of space gives a charge for that region. (Of course I am talking about points away > from the nuclei here). There is also an electrostatic potential and an electric field at that point. The relevant Gaussian keywords are CUBE and PROP. If you mean to do a calculation in which "external" point charges have been added, you can use the CHARGE keyword. --David Shobe -------------------------------------------------------------------------- From: Andrea G. Alparone Dear Sofia, You could use the Gaussian "cube" keyword to calculate electron densities or electrostatic potentials. An example for calculating the electron density can be the following (the density value at x = a, y = b and z = c cartesian-coordinates will be reported in the name.cube file): # hf / sto-3g cube=(cards,density) No title specified 0 1 a 0.000000 1.227945 0.000000 b 2.063432 -0.613973 0.000000 c -2.063432 -0.613973 0.000000 name.cube -51 a b c 1 0.0 0.0 0.0 1 0.0 0.0 0.0 1 0.0 0.0 0.0 Of course you can also evaluate grids of properties. For details I advice you to see the Gaussian user's reference or see at the following URL http://www.gaussian.com/00000430.htm. Best regards Andrea. ------------------------------------------------------------------------- From: Laurence Cuffe This is by definition Zero. However if you are looking for the electron density in a given volume near x,y,z try using the Cube command which can give you the electron density at a grid of points around the molecule. I hope this helps Laurence Cuffe -------------------------------------------------------------------------- From: Artem Masunov Sofia, Just put CHARGE keyword in command string, and x y z q after the blank line at the end of the input This will work for SP calculations only. You can also use a gaussian charge distribution instead of the point charge. See the manual http://www.gaussian.com/00000424.htm not much details there, unfotunately Hope this hepls, Artem ---------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Apr 5 10:52:53 2001 Received: from moutvdom01.kundenserver.de ([195.20.224.200]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f35EqrD02309 for ; Thu, 5 Apr 2001 10:52:53 -0400 Received: from [195.20.224.208] (helo=mrvdom01.schlund.de) by moutvdom01.kundenserver.de with esmtp (Exim 2.12 #2) id 14lB7x-0005YM-00 for chemistry@ccl.net; Thu, 5 Apr 2001 16:52:49 +0200 Received: from p3e9bbe4e.dip.t-dialin.net ([62.155.190.78] helo=anterio.internal.anterio.com) by mrvdom01.schlund.de with esmtp (Exim 2.12 #2) id 14lB7w-0005s5-00; Thu, 5 Apr 2001 16:52:48 +0200 Received: (from gerd@localhost) by anterio.internal.anterio.com (8.11.0/8.11.0) id f35ExKn07452; Thu, 5 Apr 2001 16:59:20 +0200 Date: Thu, 5 Apr 2001 16:59:20 +0200 Message-Id: <200104051459.f35ExKn07452@anterio.internal.anterio.com> X-Authentication-Warning: anterio.internal.anterio.com: gerd set sender to gerd@anterio.com using -f From: Gerd Raether To: CC: chemistry@ccl.net In-reply-to: <20010405111948.A728@cost> ((Unparsable address -- Unterminated <...> address: "Mirco Meniconi<>_^_")) Subject: Re: CCL:interation energy between molecule and probe References: <20010405111948.A728@cost> Dear Mr. Meniconi, Date: Thu, 5 Apr 2001 11:19:48 +0200 From: Mirco Meniconi <> I need to calculate with semiempirical or ab initio methods the interaction energy between a molecule and an array of probes ( like O, H2O, NH3 ecc.). with which software can I do this? you can use Jaguar - check out www.schrodinger.com. Jaguar is know for fast calculations, which seems what you need if you want to run a bunch of jobs with different probes. With Jaguar you can also get mopac if you want to use semiempirical methods. Depending where and in what kind of institution you are working you will find contact addresses at www.schrodinger.com. If you have any more questions, feel free to contact also me. We develop and distribute Schrödingers Software in Europe. Thanks, Gerd Räther -- . * www.anterio.com Gerd Räther - developer anteri o Augustaanlage 26 gerd@anterio.com * * D-68165 Mannheim +49 621 40041 -[t]33 -[f]40 From chemistry-request@server.ccl.net Thu Apr 5 12:26:20 2001 Received: from cheetah.it.wsu.edu (root@[134.121.1.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f35GQJD03256 for ; Thu, 5 Apr 2001 12:26:19 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cheetah.it.wsu.edu (8.9.3/8.9.3) with SMTP id JAA05185; Thu, 5 Apr 2001 09:25:00 -0700 (PDT) Message-ID: <00d101c0bdec$f48fa500$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Roy Jensen" , "Xavier ASSFELD" Cc: References: <157A51F55AAAD3119CD70008C7B1629DDAADDE@lvlxch01.unitedcatalysts.com> <3ACB3694.A075CF73@lctn.uhp-nancy.fr> <3ACC20DF.B5289973@lctn.uhp-nancy.fr> <85boctc85is7ou8rdr0l43ode6dr68ug7c@4ax.com> Subject: Re: CCL:symmetry change Date: Thu, 5 Apr 2001 09:24:57 -0700 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi! Looks like I missed out on all the dialogue between Roy and Xavier... At any rate, to answer Roy's question when IOP(2/16=2) is employed the H2O job crashes during the initial guess (l401.exe) immediately following the detected change in symmetry (from Cs to C2v). I think Roy is onto something by noticing the order of symmetry change is dictating the success of these jobs. My simple jobs crash when the symmetry is increased (from Cs to C2v). At least this means that, for certain jobs, we can set up our jobs intelligently and take advantage of the reduction in computation costs due to symmetry. Does anyone know of the historic reasoning why this is even an issue? I'm not a programmer but it seems like this is a programming issue. I don't know if I would call it a *feature* when my job stops because the molecular symmetry changes - a comment regarding the change in pt. group in my output file is nice but I would be quite happy if the job just kept going and finished correctly. Respectfully, Phillip Matz ----- Original Message ----- From: "Roy Jensen" To: "Xavier ASSFELD" Cc: ; Sent: Thursday, April 05, 2001 1:37 AM Subject: Re: CCL:symmetry change > The following simple job dies as stated. I am using G98W A.9. > Phillip has a H2O input file that also fails. I am curious if his also > completes a complete iteration after the symmetry change is detected > before crashing with x=2. > > Roy Jensen > > ********************************************** > #P UB3LYP/3-21G opt(verytight) IOP(2/9=222,2/16=3) > > Sample run to show problem with IOP(2/16=x) and changing symmetry. > x=1,2,3 should allow the job to continue when the symmetry changes. > This is not the case. A FIOCOM error occurs one or two iterations > after the symmetry change is detected: > x=1 or 3 dies immediately after the symmetry change is detected. > x=2 completes one itteration and then dies. > > 0 1 > H > N 1 R1 > C 2 R2 1 A1 > X 3 1. 2 90. 1 0. > O 3 R3 4 A2 1 D1 > > R1=1.00 > R2=1.20 > R3=1.19 > A1=140.7 > A2=86.2 > D1=179.9999 > ********************************************** > > > > On Thu, 05 Apr 2001 09:38:07 +0200, you wrote: > > > Roy Jensen wrote: > > > > > > I have not been able to get this IOP to work in G98W. Gaussian is > > > aware of the error; I have sent them a simple input file that fails. > > > No response yet... > > > > > > Roy Jensen > > > > > > > Instead of the NOSYM keyword, and loosing the efficiency..., you can use > > > > the > > > > keyword IOP(2/16=N) which keeps all advantages of symmetry and keep > > > > going if the point group change. > > > > If N=1 : keep going > > > > N=2 : keep going and leave symmetry on, using the old symmetry > > > > N=3 : keep going and leave symmetry on, using the new symmetry. > > > > Which value is not working? I use IOP(2/16=1) and it works perfectly, > > at least as long as I remember. Could you, please, send me the input > > file which presents this discrepancy. I am very curious about it. > > Yours. > From chemistry-request@server.ccl.net Thu Apr 5 12:42:57 2001 Received: from cheetah.it.wsu.edu (root@[134.121.1.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f35GgvD03415 for ; Thu, 5 Apr 2001 12:42:57 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cheetah.it.wsu.edu (8.9.3/8.9.3) with SMTP id JAA07224; Thu, 5 Apr 2001 09:41:36 -0700 (PDT) Message-ID: <00e901c0bdef$46768620$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Nicolas Ferre" , "Roy Jensen" , "Xavier ASSFELD" Cc: References: <157A51F55AAAD3119CD70008C7B1629DDAADDE@lvlxch01.unitedcatalysts.com> <3ACC20DF.B5289973@lctn.uhp-nancy.fr> <85boctc85is7ou8rdr0l43ode6dr68ug7c@4ax.com> <01040514124602.03306@host5> Subject: Re: CCL:symmetry change Date: Thu, 5 Apr 2001 09:41:34 -0700 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi Nicolas, Don't get me wrong here, but is it common to change the source code? I can't imagine Gaussian, Inc. thinking this is a great idea. The last thing I want to read in the literature is how someone used G98 for their calculations but they had to *massage* their source code to get the numbers they wanted. It just has bad things written all over it... Ingenious solution though, you have definitely tracked down the culprit (the rwf size) and determined a solution. The scientific method prevails, but I still feel it sets a dangerous precedence in regards to modifying commercial grade source code. We may know it is not the thing to do, but what happens to person who searches the archives 5 months from now and finds your "bug fix" solution? Respectfully, Phillip Matz ----- Original Message ----- From: "Nicolas Ferre" To: "Roy Jensen" ; "Xavier ASSFELD" Cc: ; Sent: Thursday, April 05, 2001 5:12 AM Subject: Re: CCL:symmetry change > Hi all, > In fact, it is a read-write file error. Due to the symmetry increase, the > amount of memory allocated for this rwf (579) is not sufficient. To correct > this bug, if you have access to the source code, you can add the following > lines in the link 202. In subroutine Omega, just before the line > > Call FileIO(1,-IRwNEq,InToWP(NOp2*NAtoms),NEqAtm,0) > > add > > CALL FILEIO(11,-IRWNEQ,LEN,NEqAtm,0) > IF(LEN.NE.0) THEN > LEN=INTOWP(NOP2*NATOMS)-LEN > CALL FILEIO(20,-IRWNEQ,LEN,NEqAtm,0) > ENDIF > It adjusts the length of the rwf. > The job you gave now works fine ... until it crashes because 20 optimization > steps are not enough to achieve a verytight optimization job ! > > Nicolas > > On Thursday 05 April 2001 10:37, Roy Jensen wrote: > > The following simple job dies as stated. I am using G98W A.9. > > Phillip has a H2O input file that also fails. I am curious if his also > > completes a complete iteration after the symmetry change is detected > > before crashing with x=2. > > > > Roy Jensen > > > > ********************************************** > > #P UB3LYP/3-21G opt(verytight) IOP(2/9=222,2/16=3) > > > > Sample run to show problem with IOP(2/16=x) and changing symmetry. > > x=1,2,3 should allow the job to continue when the symmetry changes. > > This is not the case. A FIOCOM error occurs one or two iterations > > after the symmetry change is detected: > > x=1 or 3 dies immediately after the symmetry change is detected. > > x=2 completes one itteration and then dies. > > > > 0 1 > > H > > N 1 R1 > > C 2 R2 1 A1 > > X 3 1. 2 90. 1 0. > > O 3 R3 4 A2 1 D1 > > > > R1=1.00 > > R2=1.20 > > R3=1.19 > > A1=140.7 > > A2=86.2 > > D1=179.9999 > > ********************************************** > > > > On Thu, 05 Apr 2001 09:38:07 +0200, you wrote: > > > Roy Jensen wrote: > > > > I have not been able to get this IOP to work in G98W. Gaussian is > > > > aware of the error; I have sent them a simple input file that fails. > > > > No response yet... > > > > > > > > Roy Jensen > > > > > > > > > Instead of the NOSYM keyword, and loosing the efficiency..., you can > > > > > use the > > > > > keyword IOP(2/16=N) which keeps all advantages of symmetry and keep > > > > > going if the point group change. > > > > > If N=1 : keep going > > > > > N=2 : keep going and leave symmetry on, using the old symmetry > > > > > N=3 : keep going and leave symmetry on, using the new symmetry. > > > > > > Which value is not working? I use IOP(2/16=1) and it works perfectly, > > > at least as long as I remember. Could you, please, send me the input > > > file which presents this discrepancy. I am very curious about it. > > > Yours. > > > > -= This is automatically added to each message by mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > > 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > > jkl@ccl.net > > -- > Nicolas FERRE > Equipe de Chimie Theorique - UMR UHP/CNRS 7565 > BP 139 - 54506 VANDOEUVRE-LES-NANCY - FRANCE > > Phone: +33 3 83 91 20 00 (ask for 35 52) > Fax : +33 3 83 91 25 30 > http://www.lctn.uhp-nancy.fr/Etudiants/Nicolas.Ferre.html > From chemistry-request@server.ccl.net Thu Apr 5 11:46:32 2001 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f35FkWD02877 for ; Thu, 5 Apr 2001 11:46:32 -0400 Sender: szilva@ribotargets.com Message-ID: <3ACC92E9.EC704685@ribotargets.com> Date: Thu, 05 Apr 2001 15:44:41 +0000 From: Szilveszter Juhos X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16-22 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: (Sad) news about insightII on Linux Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, Thank you for the many replies I've got about running this software on Linux. Unfortunatelly seems still no much choice for a Linux user, after years of requests nothing has changed at MSI :( My setup is a brand-new nVidia (Vanta), Linux based RH 7.1 and Icompiled the latest X 4.0.3 server and added nVidia support. Rasmol/VMD gives beautiful performance pity they are missing a lot of functionalities we need. Things one can do to get insightII access: i) insightII -axxess quite horrible output especially if you have to work with proteins ii) get out your new nVidia card, and buy one that is supported by the Xig servers (www.xig.com). (nVidia do not want to release some details for developers, I can not found out what is the business in that for them, so choose an other card or send mail to nVidia ten times a day. At least Xig was answering to my request not like MSI) iii) the very last chance is to try out this procedure that Malcolm (again) sent me. It was not working for me although I spent three days with chaseing sysadmin to install gcc/autoconf/etc on the SGI from freeware.sgi.com and recopiling/setting up the things, find out library dependencies (seems now it needs libX11 and libXext as well not only libm.so). You can start it without rld errors with: setenv _RLDN32_LIST $HOME/Mesa/lib/libGL.so:/usr/lib32/libm.so:DEFAULT:/usr/lib32/libX11.so:/usr/lib32/libXext.so (csh on the remote side) but still: Loading Insight II using OpenGL graphics ... XIO: fatal IO error 14 (Bad address) on X server "echo:0.0" after 34 requests (31 known processed) with 0 events remaining. .... Couldn't get initial visual in app_init_display That is all the improvement after 5 years (see the forwarded mail below). Szilva PS: apart from it have nice day ;) ----------------------------------- Malcolm Gillies wrote: Hi Szilva, [..] Unfortunately I haven't got any new information, but I'm very curious to hear what you uncover. Just after I sent out my summary, I did get the following mail, which may offer a clue as to how you might be able to get things running (see below). cheers, Malcolm -- Date: Fri, 7 Jul 2000 12:59:15 +1000 From: Drake Diedrich Subject: Re: CCL:Summary: OpenGL on Linux and Insight/Sybyl Message-ID: <20000707125915.A12514@empire.anu.edu.au> References: <200007030955.LAA12754@cmcind.pharm.uu.nl> <200007061049.MAA23637@cmcind.pharm.uu.nl> In-Reply-To: <200007061049.MAA23637@cmcind.pharm.uu.nl>; > from gillies@cmcind.pharm.uu.nl on Thu, Jul 06, 2000 at 12:49:21PM +0200 On Thu, Jul 06, 2000 at 12:49:21PM +0200, Malcolm Gillies wrote: > > Unfortunately, noone seems to have succeeded in getting MSI Insight > (aka Biosym InsightII) working with a remote Linux OpenGL display. > At first glance, this appears to be a minor problem with Insight > recognizing the remote display type correctly, but there may also be > other more subtle difficulties to overcome. I'd be interested to know > MSI's response to this problem. > In the past (Biosym '95 IIRC) I've had insightII running over the wire to a Linux box using pure Mesa with no hardware acceleration. This requires that you compile Mesa three times on the SGI (once for each -o32, -n32, -n64 compiler ABI), store the shared libraries in special directories, and then set environment variables to force insight to use MesaGL instead of the native SGI OpenGL. The remote display does not need the GLX option this way. Obviously to results are quite slow, but it did work for light use. In my case I put the environment setup in a short script and typed mesa insightII mesa ---- #!/bin/sh # libm also required due to lack of dependency support in the SGI linker # I suppose. Required by a few demo programs, larger programs probably # already link to libm. export _RLD_LIST _RLD64_LIST _RLDN32_LIST _RLD_LIST=/usr/lib/libm.so:/usr/local/Mesa/lib/libGL.so:DEFAULT _RLD64_LIST=/usr/lib64/libm.so:/usr/local/Mesa/lib64/libGL.so:DEFAULT _RLDN32_LIST=/usr/lib32/libm.so:/usr/local/Mesa/lib32/libGL.so:DEFAULT exec $* From chemistry-request@server.ccl.net Thu Apr 5 11:58:58 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f35FwwD02981 for ; Thu, 5 Apr 2001 11:58:58 -0400 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id LAA01853 for ; Thu, 5 Apr 2001 11:58:36 -0400 (EDT) Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id IAA28801 for ; Thu, 5 Apr 2001 08:58:58 -0700 (PDT) Received: from unknown(146.202.11.79) by mailhost.msi.com via smap (V2.0) id xma028794; Thu, 5 Apr 01 08:58:49 -0700 Message-Id: <5.0.2.1.2.20010405084254.00a64470@146.202.6.130> X-Sender: dgregory@146.202.6.130 X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Thu, 05 Apr 2001 08:49:07 -0700 To: chemistry@ccl.net (Comp. Chem. List) From: Don Gregory Subject: Re: CCL:structure verification In-Reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed For protein-model verification, we highly recommended Profiles-3D from Eisenberg's lab at UCLA. http://www.doe-mbi.ucla.edu/Services/Verify_3D/ http://www.doe-mbi.ucla.edu/Services/ http://www.msi.com/life/products/insight/modules/Profiles-3D_page.html Don Gregory At 03:21 PM 4/5/01 +0200, you wrote: >Dear CCLers, > >I ran a series of MD calculations on a protein, partially solvated in >water with the aim to equilibrate the solvent molecules. The equilibrated >structure is going to be employed in a docking study. > >I would like to ask for your opinions: is it valuable/necessary to check >such an equilibrated protein structure by means of tools available for >structure verification in macromulecular Xray crystalography/NMR >spectroscopy, such as WHATIF and/or ADIT from the PDB ? Are there other >programs available for this type of validation ? > >Ciao, > >Christian From chemistry-request@server.ccl.net Thu Apr 5 12:15:35 2001 Received: from fisquim.fcq.unc.edu.ar (IDENT:root@[200.16.18.35]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f35GFWD03112 for ; Thu, 5 Apr 2001 12:15:33 -0400 Received: from Adriana.fisquim.fcq.unc.edu.ar ([200.16.18.152]) by fisquim.fcq.unc.edu.ar (8.8.7/8.8.7) with SMTP id HAA05126 for ; Thu, 5 Apr 2001 07:25:18 -0300 Message-Id: <3.0.2.32.20010406002933.0074dc48@fisquim.fcq.unc.edu.ar> X-Sender: aolleta@fisquim.fcq.unc.edu.ar (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.2 (32) Date: Fri, 06 Apr 2001 00:29:33 -0300 To: Computational Chemistry Mailing List From: adriana Subject: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCL's I would very much appreciate receiving some help on how to perform "splitting scratch files across disks", while using Gaussian 98 on UNIX system. Specifically, I do not understand how a value of (-1) for the last segment works, since I have tried it thinking that it would use all the remaining available space and found out, however, that only 2050MB were used for the last segment when the available disk space was 18GB. As an alternative, I have tried splitting into smaller segments but the program recognizes only about 73 characters. Thus, the input was %rwf=/3/1,1850MB,/3/2,1850MB,/3/3,1850MB,/3/4,1850MB,/3/5,1850MB,/3/6,1850MB ,/3/,7,1850MB,/3/8,1850MB,/3/9,1850MB %mem=630MB %chk=f3clf3y.chk #T MP2/6-31G(d) Opt(CalcFC,TS) minpop nosymm but the output was %rwf=/3/1,1850MB,/3/2,1850MB,/3/3,1850MB,/3/4,1850MB,/3/5,1850MB,/3/6,1850MB ,/3/ %mem=630MB %chk=f3clf3y.chk -------------------------------------------- #T MP2/6-31G(d) Opt(CalcFC,TS) minpop nosymm -------------------------------------------- What can I do ???? Thank you very much in advance for your answers which I will eventually summarize. From chemistry-request@server.ccl.net Thu Apr 5 14:07:34 2001 Received: from hotmail.com ([209.185.241.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f35I7YD03794 for ; Thu, 5 Apr 2001 14:07:34 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 5 Apr 2001 11:04:33 -0700 Received: from 204.253.90.115 by lw3fd.law3.hotmail.msn.com with HTTP; Thu, 05 Apr 2001 18:04:32 GMT X-Originating-IP: [204.253.90.115] From: "michael donahue" To: Chemistry@ccl.net Subject: electrostatic potential surfaces of explosives Date: Thu, 05 Apr 2001 14:04:32 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 05 Apr 2001 18:04:33.0177 (UTC) FILETIME=[DE151090:01C0BDFA] Hi, Looking for some pics to demonstrate surface ionization of common explosive materials. Thanks, Mike _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com From chemistry-request@server.ccl.net Thu Apr 5 17:19:34 2001 Received: from cascara.UVic.CA (root@[142.104.5.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f35LJXD04581 for ; Thu, 5 Apr 2001 17:19:34 -0400 Received: from unix5.uvic.ca (unix5.uvic.ca [142.104.5.117]) by cascara.UVic.CA (8.11.2/8.11.2) with ESMTP id f35LIFf243362; Thu, 5 Apr 2001 14:18:15 -0700 Date: Thu, 5 Apr 2001 14:18:15 -0700 (PDT) From: Roy Jensen To: Xavier ASSFELD , cc: CCL Subject: Re: CCL:symmetry change In-Reply-To: <3ACC3DA7.17193100@lctn.uhp-nancy.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > This keyword fails when the symmetry is increased. > When the symmetry is decreased, the keyword works fine. It is interesting that IOP(2/16=2) (use old symmetry) almost works. It completes 1 itteration before crashing with a FIOCOM error. There must be some slight difference in the rwf file size, even though the symmetry remains unchanged. Regarding the modification of code. I sent this problem to Gaussian weeks ago and have not had a response. As long as Nicolas does not start selling ab initio software, he is not violating the licensing agreement (I believe). Providing the fix to Gaussian saves the programmers time and trouble. I will have to wait for the next revision of G98W. Those using Unix can modify the source code, recompile, and be on their way not having to worry about this 'feature' again. Thanks to everyone for the fruitful discussion on this topic. Roy Jensen On Thu, 5 Apr 2001, Xavier ASSFELD wrote: > Amazing! > > I tried, unsuccessfuly, to make your job run correctly. > You are right. This keyword fails when the symmetry is > increased. In all the cases I have studied so far, the > symmetry was decreased and the keyword seems to work fine. > > here follows a small example. > > # HF/STO-3G SCF=DIRECT SCAN IOP(2/16=3) > > NH3 > > 0 1 > X > N 1 1. > H 2 R 1 A > H 2 R 1 A 3 120. > H 2 R 1 A 3 240. > > R 0.9 > A 90. 3 10. From chemistry-request@server.ccl.net Thu Apr 5 20:22:38 2001 Received: from cranc02.cra.canon.com ([205.227.186.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f360MbD06108 for ; Thu, 5 Apr 2001 20:22:37 -0400 Received: by cranc02.cra.canon.com with Internet Mail Service (5.5.2653.19) id ; Thu, 5 Apr 2001 17:22:37 -0700 Message-ID: <3FD2BCBD9153D41192B100C04F1FD832067E44@cranc02.cra.canon.com> From: "Thoms, Travis" To: "Computational Chemistry List (E-mail)" Subject: Help a Gamess newbie... Date: Thu, 5 Apr 2001 17:22:31 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Greetings: I am taking the plunge into ab-initio calculations, using Gamess US. I have set up a trial run for gamess to work on, but to be quite honest, I don't quite understand what sort of information it expects for symmetry input: !enter comments here ! ! ! $CONTRL SCFTYP=RHF CITYP=NONE RUNTYP=OPTIMIZE EXETYP=CHECK ICHARG=0 ECP=NONE COORD=ZMTMPC $END $BASIS GBASIS=N21 $END $DATA TRIAL RUN cs C 00000.0000 0 00000.0000 0 00000.0000 0 0 0 0 C 00001.5125 1 00000.0000 0 00000.0000 0 1 0 0 C 00001.3212 1 00123.4130 1 00000.0000 0 2 1 0 C 00001.4253 1 00122.7597 1 00179.9998 1 3 2 1 N 00001.1407 1 00179.8250 1 00180.0813 1 4 3 2 H 00001.0813 1 00110.9581 1 00179.9997 1 1 2 3 H 00001.0845 1 00110.6745 1 00300.0425 1 1 2 3 H 00001.0845 1 00110.6746 1 00059.9568 1 1 2 3 H 00001.0737 1 00117.3431 1 00000.0000 1 2 1 6 H 00001.0734 1 00121.4331 1 00000.0000 1 3 2 1 $END The first time I ran this, there was nothing after CS, much like many of the examples in the Gamess documents. The program responded, "**** ERROR READING VARIABLE X1 CHECK COLUMN 1". I added numbers after it like "2" (out of sheer frustration) but nothing happened. I then broke down and read the instructions again. They state that for "card 3" : "For CS group, any two points in the symmetry plane." Card 4:" For CS group, one point of the symmetry plane, noncolliner with points 1 and 2." To be honest, I don't know how to format the input for these "cards" . Can someone give me an example? Thanks, Travis Thoms Research Associate Canon R&D Center Americas. inc. Telephone: 1-408-468-2864 Facsimile:1-408-468-2810 tthoms@cra.canon.com From chemistry-request@server.ccl.net Thu Apr 5 23:47:45 2001 Received: from hbond.com ([207.137.2.252]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f363liD01001 for ; Thu, 5 Apr 2001 23:47:44 -0400 Received: by hbond.com (940816.SGI.8.6.9/940406.SGI) id VAA01734; Thu, 5 Apr 2001 21:41:22 -0700 From: haney@hbond.com (Dr. David N. Haney) Message-Id: <200104060441.VAA01734@hbond.com> Subject: Re: CCL:(Sad) news about insightII on Linux To: szilva@ribotargets.com (Szilveszter Juhos) Date: Thu, 5 Apr 2001 21:41:22 -0700 (PDT) Cc: chemistry@ccl.net In-Reply-To: <3ACC92E9.EC704685@ribotargets.com> from "Szilveszter Juhos" at Apr 05, 2001 03:44:41 PM Reply-To: haney@hbond.com X-Mailer: ELM [version 2.5 PL0pre8] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Sorry I'm late here. InsightII was never intended to work over X, and it does not work very well between SGI's. It was somewhat of an accident that InsightII worked between SGI's but it required the GL service. Instead of creating true X support for InsightII they created this stripped down version -axxess. While the GL verion works reasonably well between SGI's, if you do any significant screen updates, it is very slow. Tripos does support full Sybyl over true X (it runs on a Linux system fine). While this is a nice feature, it also suffers from slow speeds if there are many screen updates. -- ######### David N. Haney, Ph.D. ######### # Haney Associates Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney@hbond.com # ################# #####################