From owner-chemistry@ccl.net Mon Apr 6 10:46:00 2009 From: "Andreea B abalaceanu_._yahoo.com" To: CCL Subject: CCL:G: problems with PBC calculation with G03 version B01 Message-Id: <-39015-090406042029-31654-i369Gg0BacCxsPJ1hK1QNw|-|server.ccl.net> X-Original-From: "Andreea B" Date: Mon, 6 Apr 2009 04:20:23 -0400 Sent to CCL by: "Andreea B" [abalaceanu^^^yahoo.com] Hello everybody! I am a Master stundent and Im currently working with Gaussian03, trying to compute PBC calculations. There is very little information available on this subject, and I would really need some help. This is my input line: %chk=arm_opt3 %mem=64mb %nproc=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=2000MB ---------------------------- # opt=tight rpbepbe/6-31g(d) ------- arm opt ------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C 0. 0. 0. H -0.1483 0.36848 -0.99354 H -0.1483 0.79469 0.70098 C 1.43408 -0.54431 0.13691 H 1.583 -0.91102 1.13101 H 1.58177 -1.34029 -0.56274 O 2.36933 0.50414 -0.1295 C 3.70123 0. 0. C 7.40247 0. 0. C 11.1037 0. 0. C 14.80493 0. 0. H 3.55293 0.36848 -0.99354 H 7.25416 0.36848 -0.99354 H 10.9554 0.36848 -0.99354 H 14.65663 0.36848 -0.99354 H 3.55293 0.79469 0.70098 H 7.25416 0.79469 0.70098 H 10.9554 0.79469 0.70098 H 14.65663 0.79469 0.70098 C 5.13531 -0.54431 0.13691 C 8.83655 -0.54431 0.13691 C 12.53778 -0.54431 0.13691 C 16.23901 -0.54431 0.13691 H 5.28423 -0.91102 1.13101 H 8.98546 -0.91102 1.13101 H 12.6867 -0.91102 1.13101 H 5.283 -1.34029 -0.56274 H 8.98423 -1.34029 -0.56274 H 12.68546 -1.34029 -0.56274 H 16.3867 -1.34029 -0.56274 O 6.07056 0.50414 -0.1295 O 9.77179 0.50414 -0.1295 O 13.47303 0.50414 -0.1295 O 17.17426 0.50414 -0.1295 C 16.45334 -1.0721 1.56767 H 15.81973 -1.91805 1.73443 H 17.47576 -1.36239 1.69132 H 16.21346 -0.30258 2.27137 Tv 18.50617 0. 0. And this is the error message I get: After all major allocation allocation failure: iend,mxcore= 6642744 6600619 Error termination via Lnk1e in C:\G03W\l502.exe at Sat Apr 04 07:54:10 2009. Job cpu time: 0 days 18 hours 24 minutes 19.0 seconds. File lengths (MBytes): RWF= 233 Int= 0 D2E= 0 Chk= 22 Scr= 1 Thank you very much in advance for your help. Andreea. abalaceanu%yahoo.com From owner-chemistry@ccl.net Mon Apr 6 14:00:01 2009 From: "Todd Keith todd-,-semichem.com" To: CCL Subject: CCL:G: AMPAC 9 with Graphical User Interface Message-Id: <-39016-090406104714-16397-1K98mofs5hVseCs+4cbV3w-x-server.ccl.net> X-Original-From: "Todd Keith" Date: Mon, 6 Apr 2009 10:47:09 -0400 Sent to CCL by: "Todd Keith" [todd(0)semichem.com] AMPAC 9 with Graphical User Interface ------------------------------------- AMPAC 9 is a major upgrade of Semichem's semiempirical quantum mechanical program, with enhancements to both QM and graphical (GUI) capabilities. AMPAC now includes PM6 and RM1 (new models), AMSOL models at NO COST to all users, and enhanced support for CI methods in solution. New GUI features expand handling of pdb files, movie production from vibrations and reaction paths, a visual MO editor and support for the latest version of Gaussian. Free demo versions are available. See details at http://www.semichem.com/ampac9 Best regards, Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER President Semichem, Inc. || Email: andy(_)semichem.com 12456 W 62nd Terr Ste D || Web:http://www.semichem.com Shawnee, KS 66216 || Phone Number: (913)268-3271 || Fax Number: (913)268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-chemistry@ccl.net Mon Apr 6 14:35:00 2009 From: "=?iso-8859-2?Q?Marek_Mal=FD?= marek.maly-x-ujep.cz" To: CCL Subject: CCL: Forcefield parameters transformation - derivation ? Message-Id: <-39017-090406123758-19942-5QLesAwJ6EbfDqGYACnAqA ~ server.ccl.net> X-Original-From: =?iso-8859-2?Q?Marek_Mal=FD?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=iso-8859-2 Date: Mon, 06 Apr 2009 17:37:59 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-2?Q?Marek_Mal=FD?= [marek.maly===ujep.cz] Dear all, I would like to simulate carbosilanes and later their complexes with organic macromolecules using Amber software. Unfortunately Amber forcefields do not contain proper ff parameters for silicon. In spite of this fact there is still possibility to simulate my Si-based molecules in Amber but I have to find proper parameters (e.g. bond, angle, dihedral) somewhere elsewhere ... I need ff parameters for Si in this contexts: C-C-C-Si, Si-O-C-C, C-Si-C-H etc. So I see here two solutions: A) To import relevant parameters from another forcefields like CVFF, PCFF, MM2, MM3 ... Regarding to this point it would be nice to have some routine which could be able to convert one forcefield file XYZ to ff file written in Amber format. If possible not to transform just text formating of the source XYZ ff file with respect of Amber formating, but also to transform properly the parameters values with respect to eventual diferences in units or analytic formulas for interatomic forces. B) To derive all the necessary parameters using some intelligent (probably quantum mechanics based) software which could be able to do this analysis for small residua provided for example in PDB format. Again would be nice to have this parameters in format compatible with Amber ff. I am kindly asking for any (even only partial) information regarding to this topic or just for redirecting to relevant information resources. Of course that I will be grateful not only for info related to some appropriate SW which can help me regarding to A) or B) but I will also appreciate any info based on own experiences, strategies, suggestions, warnings ... regarding to this topic. Best regards, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ From owner-chemistry@ccl.net Mon Apr 6 15:10:00 2009 From: "Ol Ga eurisco1**pochta.ru" To: CCL Subject: CCL:G: problems with PBC calculation with G03 version B01 Message-Id: <-39018-090406122856-19154-yYe1GfABltLLr2SCVvIS7g*o*server.ccl.net> X-Original-From: "Ol Ga" Date: Mon, 6 Apr 2009 12:28:51 -0400 Sent to CCL by: "Ol Ga" [eurisco1 ~~ pochta.ru] Dear Andreea, It is necessary to increase amount of RAM avaiable for the task. For instance, %mem=512mb. Sincerely, Ol Ga PS: #MaxDisk=2000Mb is again very strong limit. I suggest you to increase this value, too. > Sent to CCL by: "Andreea B" [abalaceanu^^^yahoo.com] > Hello everybody! > I am a Master stundent and Im currently working with Gaussian03, > trying to compute PBC calculations. There is very little information > available on this subject, and I would really need some help. > This is my input line: > %chk=arm_opt3 > %mem=64mb > %nproc=1 > Will use up to 1 processors via shared memory. > Default route: MaxDisk=2000MB > ---------------------------- > # opt=tight rpbepbe/6-31g(d) > ------- > arm opt > ------- > Symbolic Z-matrix: > Charge = 0 Multiplicity = 1 > C 0. 0. 0. > H -0.1483 0.36848 -0.99354 > H -0.1483 0.79469 0.70098 > C 1.43408 -0.54431 0.13691 > H 1.583 -0.91102 1.13101 > H 1.58177 -1.34029 -0.56274 > O 2.36933 0.50414 -0.1295 > C 3.70123 0. 0. > C 7.40247 0. 0. > C 11.1037 0. 0. > C 14.80493 0. 0. > H 3.55293 0.36848 -0.99354 > H 7.25416 0.36848 -0.99354 > H 10.9554 0.36848 -0.99354 > H 14.65663 0.36848 -0.99354 > H 3.55293 0.79469 0.70098 > H 7.25416 0.79469 0.70098 > H 10.9554 0.79469 0.70098 > H 14.65663 0.79469 0.70098 > C 5.13531 -0.54431 0.13691 > C 8.83655 -0.54431 0.13691 > C 12.53778 -0.54431 0.13691 > C 16.23901 -0.54431 0.13691 > H 5.28423 -0.91102 1.13101 > H 8.98546 -0.91102 1.13101 > H 12.6867 -0.91102 1.13101 > H 5.283 -1.34029 -0.56274 > H 8.98423 -1.34029 -0.56274 > H 12.68546 -1.34029 -0.56274 > H 16.3867 -1.34029 -0.56274 > O 6.07056 0.50414 -0.1295 > O 9.77179 0.50414 -0.1295 > O 13.47303 0.50414 -0.1295 > O 17.17426 0.50414 -0.1295 > C 16.45334 -1.0721 1.56767 > H 15.81973 -1.91805 1.73443 > H 17.47576 -1.36239 1.69132 > H 16.21346 -0.30258 2.27137 > Tv 18.50617 0. 0. > And this is the error message I get: > After all major allocation allocation failure: iend,mxcore= 6642744 6600619 > Error termination via Lnk1e in C:\G03W\l502.exe at Sat Apr 04 07:54:10 2009. > Job cpu time: 0 days 18 hours 24 minutes 19.0 seconds. > File lengths (MBytes): RWF= 233 Int= 0 D2E= 0 Chk= 22 Scr= 1 > Thank you very much in advance for your help. > Andreea. From owner-chemistry@ccl.net Mon Apr 6 18:03:01 2009 From: "aps1968##googlemail.com" To: CCL Subject: CCL:G: Iodine basis set Message-Id: <-39019-090406163725-2371-oab1k5oxj7QLCPJxQvmK3A(~)server.ccl.net> X-Original-From: aps1968%x%googlemail.com Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 6 Apr 2009 22:07:25 +0200 MIME-Version: 1.0 Sent to CCL by: aps1968/./googlemail.com Dear colleagues, I want to perform a geometry optimization in Gaussian 03 (HF, B3LYP) of certain molecules containing Iodine, using basis set TZVP. It appears that Iodine is not included. What can I do? Cheers, Andrzej From owner-chemistry@ccl.net Mon Apr 6 20:43:00 2009 From: "Cristian V. Diaconu cvdiaconu-$-rice.edu" To: CCL Subject: CCL:G: problems with PBC calculation with G03 version B01 Message-Id: <-39020-090406202402-28879-2Z2evf40bvRHciCvbCNepA:+:server.ccl.net> X-Original-From: "Cristian V. Diaconu" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 06 Apr 2009 18:47:26 -0500 MIME-Version: 1.0 Sent to CCL by: "Cristian V. Diaconu" [cvdiaconu-#-rice.edu] Looks like you are low on memory. Try increasing %mem, and please use #p to start route, so you get more info. Try setting %mem= to half or your computer RAM, and increase it up to 3/4 if that fails. Do not use more than about 3/4 of your computer memory because the calculation will become unreasonably slow. Chris Andreea B abalaceanu_._yahoo.com wrote: > Sent to CCL by: "Andreea B" [abalaceanu^^^yahoo.com] > Hello everybody! > > I am a Master stundent and Im currently working with Gaussian03, trying to compute PBC calculations. There is very little information available on this subject, and I would really need some help. > This is my input line: > > %chk=arm_opt3 > %mem=64mb > %nproc=1 > Will use up to 1 processors via shared memory. > Default route: MaxDisk=2000MB > ---------------------------- > # opt=tight rpbepbe/6-31g(d) > ------- > arm opt > ------- > Symbolic Z-matrix: > Charge = 0 Multiplicity = 1 > C 0. 0. 0. > H -0.1483 0.36848 -0.99354 > H -0.1483 0.79469 0.70098 > C 1.43408 -0.54431 0.13691 > H 1.583 -0.91102 1.13101 > H 1.58177 -1.34029 -0.56274 > O 2.36933 0.50414 -0.1295 > C 3.70123 0. 0. > C 7.40247 0. 0. > C 11.1037 0. 0. > C 14.80493 0. 0. > H 3.55293 0.36848 -0.99354 > H 7.25416 0.36848 -0.99354 > H 10.9554 0.36848 -0.99354 > H 14.65663 0.36848 -0.99354 > H 3.55293 0.79469 0.70098 > H 7.25416 0.79469 0.70098 > H 10.9554 0.79469 0.70098 > H 14.65663 0.79469 0.70098 > C 5.13531 -0.54431 0.13691 > C 8.83655 -0.54431 0.13691 > C 12.53778 -0.54431 0.13691 > C 16.23901 -0.54431 0.13691 > H 5.28423 -0.91102 1.13101 > H 8.98546 -0.91102 1.13101 > H 12.6867 -0.91102 1.13101 > H 5.283 -1.34029 -0.56274 > H 8.98423 -1.34029 -0.56274 > H 12.68546 -1.34029 -0.56274 > H 16.3867 -1.34029 -0.56274 > O 6.07056 0.50414 -0.1295 > O 9.77179 0.50414 -0.1295 > O 13.47303 0.50414 -0.1295 > O 17.17426 0.50414 -0.1295 > C 16.45334 -1.0721 1.56767 > H 15.81973 -1.91805 1.73443 > H 17.47576 -1.36239 1.69132 > H 16.21346 -0.30258 2.27137 > Tv 18.50617 0. 0. > > And this is the error message I get: > > After all major allocation allocation failure: iend,mxcore= 6642744 6600619 > Error termination via Lnk1e in C:\G03W\l502.exe at Sat Apr 04 07:54:10 2009. > Job cpu time: 0 days 18 hours 24 minutes 19.0 seconds. > File lengths (MBytes): RWF= 233 Int= 0 D2E= 0 Chk= 22 Scr= 1 > > Thank you very much in advance for your help. > > Andreea. > > abalaceanu ~ yahoo.com> > > > -- Cristian V. Diaconu Postdoctoral Research Associate Department of Chemistry - MS60 Rice University PO Box 1892 Houston, TX 77251-1892 Phone: 713-348-3734 Email: cvdiaconu.:+:.rice.edu