From owner-chemistry@ccl.net Wed May 27 00:15:00 2009 From: "TJ O Donnell tjo[A]gnova.com" To: CCL Subject: CCL: Mol2 file example? Message-Id: <-39384-090526221443-1102-6FSp5qT5fshJ0OD9khptIQ-*-server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 26 May 2009 18:30:50 -0700 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo^^^gnova.com] I just used openbabel to convert 10MH.pdb to 10MH.sy2 It appears to have ligands and water, though I had to add hydrogens to get the waters to be included. Joe, I can't attach a file here, so send me an email and I'll send the file to you. TJ -- TJ O'Donnell, Ph.D. President, gNova, Inc. http://www.gnova.com > Joe Leonard jleonard42__gmail.com wrote: >> >> Sent to CCL by: Joe Leonard [jleonard42*|*gmail.com] >> Folks, does anybody have (or can they easily generate) a Sybyl mol2 file containing a protein/ligand and waters? Any old PDB file would do, as long as it's a cocrystal with waters. While the mol2 file format is documented on their support website, there's no example file. There's a fair number of entries that would profit from a more-complete example such as the one I'm looking for... >> >> Thanks in advance! I've tried googling for such an example and I'm getting papers talking about files rather than the files themselves... >> >> Joe Leonard >> jleonard42],[gmail.com >> -- >> The only solution I see for developers to not have to be diplomatic to get cooperation from other departments is to arm the developers. >> From owner-chemistry@ccl.net Wed May 27 05:15:01 2009 From: "Barbara Jagoda-Cwiklik barbara#%#fh.huji.ac.il" To: CCL Subject: CCL:G: NON-equilibrium PCM calculation in Gaussian Message-Id: <-39385-090527044630-28294-5PjRBQfkPhTV3Tai6Kuqpw=server.ccl.net> X-Original-From: Barbara Jagoda-Cwiklik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 27 May 2009 11:46:16 +0300 MIME-Version: 1.0 Sent to CCL by: Barbara Jagoda-Cwiklik [barbara]|[fh.huji.ac.il] Hi Jan, Of course they are - just in the keywords line use any functional you want ("# blyp/" instead of "# hf/" as it was in examples). If you are interested in VIP and AIP difference you shall employ NonEq keyword to get VIP. Than you shall run two separate jobs (or at least I was doing so) to get AIP - one job for your metal complex and the second one for the complex where one electron was detached. I you need more "help" just write me. Best, Basia On Tue, May 26, 2009 at 11:52 PM, Jan Moens molukken#hotmail.com wrote: > > Sent to CCL by: "Jan Moens" [molukken{:}hotmail.com] > Thank you Basia for your response! > I previously saw your interesting paper and I was wondering if these type of calculations are also possible with DFT (no TD-DFT) instead of the MP or derivative methods , within the G03 version? > In particular, I am interested in differences between vertical and adiabatic ionization potentials of metal complexes, where solvent is modelled by pcm. > > best regards > Jan Moens >> "Barbara Jagoda-Cwiklik barbara[a]fh.huji.ac.il" wrote: >> >> Sent to CCL by: Barbara Jagoda-Cwiklik [barbara]*[fh.huji.ac.il] >> Dear Jan, >> >> NonEq can take two arguments: NonEq=3Dwrite and NonEq=3Dread. In the first >> case PCM parameters are written to the checkpoint file, in the second >> - they are read from the checkpoint (simply speaking, the cavity read >> > from the disk is used). >> Take a look at a test job: http://g03.sownar.com/test614.gjf >> We employed a similar scheme in: J. Phys. Chem. A, Vol. 112 (2008) 3499 >> >> Best, >> Basia >> >> On Mon, May 25, 2009 at 4:42 PM, Jan Moens molukken*_*hotmail.com >> wrote: >> > >> > Sent to CCL by: "Jan =A0Moens" [molukken^hotmail.com] >> > Dear all, >> > >> > I am interested in nonequilibrium PCM calculations for vertical ionizatio= >> n potentials. In the g03 manual, it is indicated that non equilibrium solva= >> tion can be performed using the NonEq=3Dtype PCM keyword. But this keyword = >> is not described elsewhere in the manual. Does anyone know how to use this = >> keyword in a correct way? >> > >> > Thanks in advance >> > >> > Jan Moens >> > PhD student >> > Vrije Universiteit Brussel >> > >> > >> > >> > -=3D This is automatically added to each message by the mailing script = >> =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> >> > >> > >> >> >> >> --=20 >> Barbara Jagoda-Cwiklik, Ph.D >> The Fritz Haber Research Center for Molecular Dynamics >> Institute of Chemistry >> The Hebrew University of Jerusalem >> Jerusalem, ISRAEL >> e-mail: barbara#,#fh.huji.ac.il> > > -- Barbara Jagoda-Cwiklik, Ph.D The Fritz Haber Research Center for Molecular Dynamics Institute of Chemistry The Hebrew University of Jerusalem Jerusalem, ISRAEL e-mail: barbara::fh.huji.ac.il From owner-chemistry@ccl.net Wed May 27 05:39:00 2009 From: "Geoffrey Hutchison geoffh^pitt.edu" To: CCL Subject: CCL: Mol2 file example? Message-Id: <-39386-090527004556-15436-+kLRHPYrfJDI8PzOibj/hg-$-server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Type: multipart/alternative; boundary=Apple-Mail-4-949905226 Date: Wed, 27 May 2009 00:13:13 -0400 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: Geoffrey Hutchison [geoffh-,-pitt.edu] --Apple-Mail-4-949905226 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit > Hi Joe, Open Babel can convert pdb files to mol2 easily enough, http://openbabel.org/wiki/Main_Page > . > Ben. Well Joe knows that pretty well -- I can vouch that he's a long time Open Babel user. I think he wants an "authentic" mol2 file. Open Babel does try to stick to published file format specifications, but there's a difference between a specification and having some example files. For example, consider the difference between the HTML specifications and a bunch of web pages. I'd also be happy to have some example mol2 files straight from Sybyl. Cheers, -Geoff --- Prof. Geoffrey Hutchison Assistant Professor, Department of Chemistry University of Pittsburgh http://hutchison.chem.pitt.edu/ Office: (412) 648-0492 --Apple-Mail-4-949905226 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable
Hi= Joe, Open Babel can convert pdb files to mol2 easily enough, http://openbabel.org/wiki/Mai= n_Page.
Ben.

Well Joe knows that = pretty well -- I can vouch that he's a long time Open Babel user. I = think he wants an "authentic" mol2 file. Open Babel does try to stick to = published file format specifications, but there's a difference between a = specification and having some example files. For example, consider the = difference between the HTML specifications and a bunch of web = pages.

I'd also be happy to have some example = mol2 files straight from = Sybyl.

Cheers,
-Geoff

---
Prof. Geoffrey = Hutchison
Assistant Professor, Department of = Chemistry
University of Pittsburgh
 =

= --Apple-Mail-4-949905226-- From owner-chemistry@ccl.net Wed May 27 06:45:01 2009 From: "Van Dam, HJJ \(Huub\) huub.van-dam-.-stfc.ac.uk" To: CCL Subject: CCL: Modifications of Hartree-Fock / Density Matrix Functional Theory / Ensembles Message-Id: <-39387-090525183831-22453-c7QS/mImtPmBxmPzNWNOgg*_*server.ccl.net> X-Original-From: "Van Dam, HJJ \(Huub\)" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 25 May 2009 22:25:19 +0100 MIME-Version: 1.0 Sent to CCL by: "Van Dam, HJJ \(Huub\)" [huub.van-dam[a]stfc.ac.uk] Dear Colleagues, It is well known that the Hartree-Fock energy expression is only correct for single determinant wavefunctions or equivalently idem-potent density matrixes. For other N-representable density matrices the energy comes out too high. It is possible to address this issue at least to some extent. However, it would seem to me that various attempts to fix this issue will have been tried in the past. I would be grateful if anyone could point me to some references on this matter, please. Thank you, Huub van Dam ======================================================================== Huub van Dam huub.van-dam]~[stfc.ac.uk Science and Technology Facilities Council phone: +44-1925-603933 Daresbury Laboratory fax: +44-1925-603634 Daresbury Science and Innovation Campus Daresbury, Warrington WA4 4AD ======================================================================== From owner-chemistry@ccl.net Wed May 27 08:46:01 2009 From: "Rosa Weber rosa.weber~!~scienomics.com" To: CCL Subject: CCL: THE FUTURE OF MOLECULAR MODELING IN INDUSTRIAL R&D Message-Id: <-39388-090527084021-28456-BZ3ZruyQLjACxJ1vDIoyRw_._server.ccl.net> X-Original-From: Rosa Weber Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 27 May 2009 14:34:59 +0200 MIME-Version: 1.0 Sent to CCL by: Rosa Weber [rosa.weber(0)scienomics.com] Dear All, Scienomics invites you to a world wide webinar on June 11th 2009 at 4:00pm (CEST), where our scientists will demonstrate how Scienomics' simulation technology can generate valuable data for your R&D projects and reduce experimental time and investment. MAPS is a commercial molecular simulations platform for materials science and combines open source and proprietary modeling tools, like for example, LAMMPS, Towhee, NAMD, ABINIT, MNDO, SciDPD and more. Applications of MAPS based simulation technology range from the calculation of friction coefficients for lubricants over mechanical properties for nanocomposites to critical micelle concentrations for the home and personal care industry. Additionally, Scienomics' physical properties engine, SciTherm which allows equation of state type of modeling will be presented. The focus here will be given to applications in gas separations as well as solubility prediction of pharmaceuticals directly from their molecular structure. 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For any additional information, please contact Rosa Weber at +49 231 135 8088. Cordially, Rosa Weber, Scienomics From owner-chemistry@ccl.net Wed May 27 09:21:00 2009 From: "Reinaldo Pis Diez reinaldo.pisdiez#%#gmail.com" To: CCL Subject: CCL: Modifications of Hartree-Fock / Density Matrix Functional Theory / Ensembles Message-Id: <-39389-090527085552-746-wtWlVHk+9omoiCTBm+CnrA,,server.ccl.net> X-Original-From: Reinaldo Pis Diez Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 27 May 2009 08:51:25 -0300 MIME-Version: 1.0 Sent to CCL by: Reinaldo Pis Diez [reinaldo.pisdiez(0)gmail.com] Dear Huub, Have a look at the former work of Eduardo Ludeña and Eugene Kryachko. They've worked a lot on the concepts of both N- and v-representable densities. Regards, Reinaldo Van Dam, HJJ (Huub) huub.van-dam-.-stfc.ac.uk escribió: > Sent to CCL by: "Van Dam, HJJ \(Huub\)" [huub.van-dam[a]stfc.ac.uk] > > Dear Colleagues, > > It is well known that the Hartree-Fock energy expression is only correct > for single determinant wavefunctions or equivalently idem-potent density > matrixes. For other N-representable density matrices the energy comes > out too high. It is possible to address this issue at least to some > extent. However, it would seem to me that various attempts to fix this > issue will have been tried in the past. I would be grateful if anyone > could point me to some references on this matter, please. > > Thank you, > > Huub van Dam > > > ======================================================================== > Huub van Dam huub.van-dam-x-stfc.ac.uk > Science and Technology Facilities Council phone: +44-1925-603933 > Daresbury Laboratory fax: +44-1925-603634 > Daresbury Science and Innovation Campus > Daresbury, Warrington > WA4 4AD > ========================================================================> > > From owner-chemistry@ccl.net Wed May 27 10:14:01 2009 From: "Joseph M Leonard jleonard42!^!gmail.com" To: CCL Subject: CCL: mol2 file query #2 Message-Id: <-39390-090527101006-20070-R6cEZOo9VJ6BOkPShslaeg#%#server.ccl.net> X-Original-From: Joseph M Leonard Content-Type: multipart/alternative; boundary=001636eef86b69f1af046ae4f676 Date: Wed, 27 May 2009 09:38:45 -0400 MIME-Version: 1.0 Sent to CCL by: Joseph M Leonard [jleonard42]![gmail.com] --001636eef86b69f1af046ae4f676 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Thanks for the responses, which I'll summarize this evening! A few more (easy?) questions: 1) Anybody know the number/name correspondence regarding dictionaries? The sample files I've been sent mention 'macromol' and have a 4 as the dictionary id in the ,,SUBSTRUCTURE entries. I've seen 1 as the ID - is zero valid, particularly as a marker for non-dictionary groups? Does this number matter if there's no ,,DICT entry in the file? 2) Is there a distinction between BIOPOLYMER, PROTEIN and NUCLEIC_ACID molecule types? Are the latter two used when it's only amino acids or nucleic acids and the former used when there's a mixture or non-macromolecular groups present? Does it matter - or can one always use BIOPOLYMER vs. SMALL? Thanks! Joe -- The only solution I see for developers to not have to be diplomatic to get cooperation from other departments is to arm the developers. --001636eef86b69f1af046ae4f676 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks for the responses, which I'll summarize this evening!

A f= ew more (easy?) questions:

1) Anybody know the number/name correspon= dence regarding dictionaries?=A0 The sample files I've been sent mentio= n 'macromol' and have a 4 as the dictionary id in the ,,<TRIPOS&g= t;SUBSTRUCTURE entries.=A0 I've seen 1 as the ID - is zero valid, parti= cularly as a marker for non-dictionary groups?=A0 Does this number matter i= f there's no ,,<TRIPOS>DICT entry in the file?

2) Is there a distinction between BIOPOLYMER, PROTEIN and NUCLEIC_ACID = molecule types?=A0 Are the latter two used when it's only amino acids o= r nucleic acids and the former used when there's a mixture or non-macro= molecular groups present?=A0 Does it matter - or can one always use BIOPOLY= MER vs. SMALL?

Thanks!

Joe

--
The only solution I see = for developers to not have to be diplomatic to get cooperation from other d= epartments is to arm the developers.

--001636eef86b69f1af046ae4f676-- From owner-chemistry@ccl.net Wed May 27 18:30:01 2009 From: "Esteban Gabriel Vega Hissi egvega+*+gmail.com" To: CCL Subject: CCL:G: Huge Number of Basis Functions Message-Id: <-39391-090527122357-3406-EAB/jkHCwRf76aUv791/SA++server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=0016e6dd89e8ab50af046ae6580b Date: Wed, 27 May 2009 12:17:49 -0300 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega##gmail.com] --0016e6dd89e8ab50af046ae6580b Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi CCL readers, Is it possible to perform a single point (energy) calculation with gaussian03 of a 78 atoms system with about 2800 basis functions or am I dreaming? The level of calculation I require is: MP2(FC)/aug-cc-pVTZ I hope you can help me. Thanks in advance Best wishes Biochemist Esteban Gabriel Vega Hissi UNSL Argentina --0016e6dd89e8ab50af046ae6580b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi CCL readers,

Is it possible to perform a single point (energy) calculation with gaussian03 of a 78 atoms system with about 2800 basis functions or am I dreaming?
The level of calculation I require is: MP2(FC)/aug-cc-pVTZ

I hope you can help me.
Thanks in advance
Best wishes

Biochemist Esteban Gabriel Vega Hissi
UNSL
Argentina
--0016e6dd89e8ab50af046ae6580b-- From owner-chemistry@ccl.net Wed May 27 23:01:01 2009 From: "Henry Martinez hmartine\a/gmail.com" To: CCL Subject: CCL:G: simple butane calculation. Rotation energy barrier. Gaussian Message-Id: <-39392-090527225859-21803-u3mJlqaW0h+vwaGqKTlRPA+/-server.ccl.net> X-Original-From: "Henry Martinez" Date: Wed, 27 May 2009 22:58:55 -0400 Sent to CCL by: "Henry Martinez" [hmartine*gmail.com] I would like to calculate with a good aprox. the Rotation energy barrier for butane. So, I have to calculate the structure with the two methyl anti (180), then 120 (eclipse), then 60 (Gauche), and finally 0 degrees (eclipse). The question is: For each geometry I should calculate the OPTIMIZATION using a keyword to do not change the geometry so much (I think that at some point it will try to go to the anti geometry, dont?) or I just calculate the energy for that particular geometry (I alredy tried that but the results were not close, so may be I am missing something) . I am using Gaussian 03, HF/6-31g*. Is there any other way to do it. Can anyone explain me how to do it? Thanks a lot