From owner-chemistry@ccl.net Wed Apr 28 13:01:00 2010 From: "andras.borosy||givaudan.com" To: CCL Subject: CCL:G: Linux vs Windows Message-Id: <-41721-100428100310-30885-psMgBoIupoJh4Rqybl692g%server.ccl.net> X-Original-From: andras.borosy%givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 004A2B14C1257713_=" Date: Wed, 28 Apr 2010 15:30:08 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy : givaudan.com This is a multipart message in MIME format. --=_alternative 004A2B14C1257713_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Albert, 1) I have no experience with comparison of Gaussian at Windows and Linux,=20 but I have never seen (in the last 15 years) any computation-intensive=20 application which runs at Windows better. 2) I do have experience with comparison of Gaussian and other QC=20 applications (PQS, Turbomole and GAMESS). Gaussian is the slowest. Best wishes, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Albert Poater albertpo##stark.udg.es" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com,ccl.net 23.04.2010 14:49 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL:G: Linux vs Windows Sent to CCL by: "Albert Poater" [albertpo^-^stark.udg.es] Dear CCL users, Does anybody any experience with the performance of Gaussian with the Window platform (not XP, I mean the professional version that does not contain graphical applications)? I am pretty sure that the performance is much slower with respect to Linux but which is the percentage and the main doubt is if Windows is stable or not tu run Gaussian. Which is the performance for clusters with blades with nodes of two QUAD-cores? Thanks in advance, Albert -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 004A2B14C1257713_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Albert,

1) I have no experience with compari= son of Gaussian at Windows and Linux, but I have never seen (in the last 15 years) any computation-intensive application which runs at Windows better.<= /font>

2) I do have experience with compari= son of Gaussian and other QC  applications (PQS, Turbomole and GAMESS). Gaussian is the slowest.

Best wishes,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com




"Albert Poater a= lbertpo##stark.udg.es" <owner-chemistry,ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com,ccl.net

23.04.2010 14:49
Please respond to
"CCL Subscribers" <chemistry,ccl.net>
To
"Borosy, Andras " <andras.borosy,givaudan.com>
cc
Subject
CCL:G: Linux vs Windows





Sent to CCL by: "Albert  Poater" [albertpo^-^stark.udg.es] Dear CCL users,
Does anybody any experience with the performance of Gaussian with the
Window platform (not XP, I mean the professional version that does not
contain graphical applications)? I am pretty sure that the performance is
much slower with respect to Linux but which is the percentage and the main<= br> doubt is if Windows is stable or not tu run Gaussian. Which is the
performance for clusters with blades with nodes of two QUAD-cores?
Thanks in advance,
Albert



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--=_alternative 004A2B14C1257713_=-- From owner-chemistry@ccl.net Wed Apr 28 14:08:00 2010 From: "Alfredo Tlahuice tlahuicef() yahoo.com" To: CCL Subject: CCL:G: B3LYP and def2-TZVP Message-Id: <-41722-100428140703-30355-2X83GAVIEedvRl+Xn+blrQ]_[server.ccl.net> X-Original-From: "Alfredo Tlahuice" Date: Wed, 28 Apr 2010 14:07:02 -0400 Sent to CCL by: "Alfredo Tlahuice" [tlahuicef===yahoo.com] Hi there I want to start a gaussian 03 calculation using the def2-TZVP basis. So my question is how can I define that basis set in G03? Thanks in advance. From owner-chemistry@ccl.net Wed Apr 28 14:43:00 2010 From: "Ronald L Cook cookrl%a%tda.com" To: CCL Subject: CCL: Bulding a Chemical database Message-Id: <-41723-100428135529-12051-KHIFoPfBwp2c13Y7XL4TnA,+,server.ccl.net> X-Original-From: "Ronald L Cook" Date: Wed, 28 Apr 2010 13:55:27 -0400 Sent to CCL by: "Ronald L Cook" [cookrl() tda.com] Hi All We are carrying out a comprehensive computational study of a series of molecules including optimization and property calculations at the RB3LYP 6-311++F(d,p) level to generate QM descriptors. We are also calculating MEP maps, charges on atoms, and Fukui indices using Hirshfeld population analysis. We would also like to store graphics of the the optimized structures. When we started out we were using Excel to store and probe the results. This has gotten quite unwieldly. Does anyone have any recommendations for the best database software (e.q. Access or software more directed to chemists)? Or can anyone recommend a good book on building a chemical database from Access or the various forms of SQL software. Thanks in Advance for your advise Ronald Cook Principal Scientist TDA research, Inc. From owner-chemistry@ccl.net Wed Apr 28 17:29:00 2010 From: "John McKelvey jmmckel^^^gmail.com" To: CCL Subject: CCL:G: B3LYP and def2-TZVP Message-Id: <-41724-100428155723-14437-Ptl2tobLuBvaufR1Y79Dhw _ server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 28 Apr 2010 15:57:08 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel++gmail.com] Partial answer: In the TURBOMOLE basis set directory it is pointed out that def2-TZVP basis is the same as TZVPP. If that is not available in Gaussian it might be possible to get it from the PNL web site. John McKelvey On Wed, Apr 28, 2010 at 2:07 PM, Alfredo Tlahuice tlahuicef() yahoo.com wrote: > > Sent to CCL by: "Alfredo =A0Tlahuice" [tlahuicef=3D=3D=3Dyahoo.com] > Hi there > I want to start a gaussian 03 calculation using the def2-TZVP basis. > So my question is how can I define that basis set in G03? > > Thanks in advance. > > > > -=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 John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel:_:gmail.com From owner-chemistry@ccl.net Wed Apr 28 18:04:00 2010 From: "Carlos Alberto Ortega caoz96**yahoo.es" To: CCL Subject: CCL: How i do to model a protein which sequence no have a homologue in PDB? Message-Id: <-41725-100428162510-19776-BBkg+rJ+WRfzk1XlkoZxTw+*+server.ccl.net> X-Original-From: "Carlos Alberto Ortega" Date: Wed, 28 Apr 2010 16:25:09 -0400 Sent to CCL by: "Carlos Alberto Ortega" [caoz96:yahoo.es] How i do to model a protein which sequence no have a homologue in PDB? The complete sequence no have a homologue in PDB, only have a homologue for a part of the sequenece, and the rest no have homologues. I take the structure which is homologue a seccion of the sequence and try to model in server webs, but the protein model is not very well for my judgment. I use the server I-TASSER server, swissmodel, MODELLER and i try to use the FUGUE in Sybyl, but how i known which is the best model? and can i use this model for docking? Thanks very much for your help. From owner-chemistry@ccl.net Wed Apr 28 18:39:01 2010 From: "Vlad vvv900|,|anusf.anu.edu.au" To: CCL Subject: CCL: Bulding a Chemical database Message-Id: <-41726-100428171552-2343-uUtQ0sDhHdMOb7NI6DtZKA^server.ccl.net> X-Original-From: Vlad Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1251; format=flowed Date: Thu, 29 Apr 2010 06:34:01 +1000 MIME-Version: 1.0 Sent to CCL by: Vlad [vvv900*anusf.anu.edu.au] Hi Ronald, If you're really serious about databasing and your study takes a data-centric turn you should probably switch to the relational databases. MySQL data server is probably the best candidate. Of course, you'll need to invest some time into learning SQL and some basic ideas of the database design. But it's much simpler than quantum chemistry. :) Of course, you'll need (friendly) interface for the database. The web browser interface is probably the best. PHP and Ruby are probably the simplest to start with. But Java is probably better. Moreover, in the case of Java you can build both server (web interface) and desktop (GUI program) side applications and reuse the same Java libraries. Regards, Vlad Dr. Vladislav Vasilyev National Facility, ANU Canberra, Australia > We are carrying out a comprehensive computational study of a series > of molecules including optimization and property calculations at the > RB3LYP 6-311++F(d,p) level to generate QM descriptors. We are also > calculating MEP maps, charges on atoms, and Fukui indices using > Hirshfeld population analysis. We would also like to store graphics > of the the optimized structures. > > When we started out we were using Excel to store and probe the > results. This has gotten quite unwieldly. Does anyone have any > recommendations for the best database software (e.q. Access or > software more directed to chemists)? Or can anyone recommend a good > book on building a chemical database from Access or the various forms > of SQL software. From owner-chemistry@ccl.net Wed Apr 28 19:14:00 2010 From: "Adam Tenderholt atenderholt[#]gmail.com" To: CCL Subject: CCL: Bulding a Chemical database Message-Id: <-41727-100428182838-30903-lKNveFt+aXAj3qX5meW6pA-.-server.ccl.net> X-Original-From: Adam Tenderholt Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 28 Apr 2010 14:24:54 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt,gmail.com] I can think of a couple of factors that you should probably mention or be thinking about before deciding on which software to go with. -Will the database be edited by multiple people? How many people will be accessing the database (read-only)? -Does the database need to be functioning ASAP or do you have time to look for a more elegant solution? -Do you want versioning or a history of changes made to the database? I think there's also an open source project to build a database platform similar to what you're after, but I can't remember its name. Maybe look on sites like sourceforge.net and freshmeat.net? Adam On Wed, Apr 28, 2010 at 1055 AM, Ronald L Cook cookrl%a%tda.com wrote: > > Sent to CCL by: "Ronald L Cook" [cookrl() tda.com] > Hi All > > We are carrying out a comprehensive computational study of a series of mo= lecules including optimization and property calculations at the RB3LYP 6-31= 1++F(d,p) level to generate QM descriptors. =A0We are also calculating MEP = maps, charges on atoms, and Fukui indices using Hirshfeld population analys= is. =A0We would also like to store graphics of the the optimized structures= . > > When we started out we were using Excel to store and probe the results. = =A0This has gotten quite unwieldly. =A0Does anyone have any recommendations= for the best database software (e.q. Access or software more directed to c= hemists)? =A0Or can anyone recommend a good book on building a chemical dat= abase from Access or the various forms of SQL software. > > Thanks in Advance for your advise > > Ronald Cook > Principal Scientist > TDA research, Inc. > > > > -=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> > > From owner-chemistry@ccl.net Wed Apr 28 21:18:00 2010 From: "Geoffrey Hutchison geoffh|,|pitt.edu" To: CCL Subject: CCL: Bulding a Chemical database Message-Id: <-41728-100428170016-5451-6LdHSKZHjO494/grsOku8Q(!)server.ccl.net> X-Original-From: Geoffrey Hutchison Content-transfer-encoding: quoted-printable Content-type: text/plain; charset=us-ascii Date: Wed, 28 Apr 2010 16:03:30 -0400 MIME-version: 1.0 (Apple Message framework v1078) Sent to CCL by: Geoffrey Hutchison [geoffh*pitt.edu] On Apr 28, 2010, at 1:55 PM, Ronald L Cook cookrl%a%tda.com wrote: > When we started out we were using Excel to store and probe the = results. This has gotten quite unwieldly. Does anyone have any = recommendations for the best database software (e.q. Access or software = more directed to chemists)? Or can anyone recommend a good book on = building a chemical database from Access or the various forms of SQL = software. TJ O'Donnell has written such a book. "Design and Use of Relational = Databases in Chemistry" http://www.gnova.com/book/ There are several existing chemical database systems, mainly using SQL. = Several of these are open source (pgchem::tigress, MyChem, etc.) Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh##pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Wed Apr 28 22:20:00 2010 From: "Rajarshi Guha rajarshi.guha:_:gmail.com" To: CCL Subject: CCL: Bulding a Chemical database Message-Id: <-41729-100428212502-8332-NOMRagMlHv97xt5EuExcvQ.:.server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Wed, 28 Apr 2010 20:32:44 -0400 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Rajarshi Guha [rajarshi.guha|*|gmail.com] On Apr 28, 2010, at 1:55 PM, Ronald L Cook cookrl%a%tda.com wrote: > > Sent to CCL by: "Ronald L Cook" [cookrl() tda.com] > Hi All > > We are carrying out a comprehensive computational study of a series > of molecules including optimization and property calculations at the > RB3LYP 6-311++F(d,p) level to generate QM descriptors. We are also > calculating MEP maps, charges on atoms, and Fukui indices using > Hirshfeld population analysis. We would also like to store graphics > of the the optimized structures. There are a number of ways you could approach this, depending on what you need out of such a solution. Pretty much an SQL database (MySQL, Postgres) will solve your problem Since a number of your queries will be atom centric, it might be useful to explicitly store atoms (i.e., rows would be atoms). Of course this would not necessarily store connectivity, so you might store the actual structure (either as a string or else as a BLOB) so you can pull it out and manipulate the structure directly. A separate table could be used to store molecule-level descriptors (as opposed to atom-level descriptors). It'd also be useful to store the calculation parameters/protocol along with the structures - in the long term this would let you automatically rerun calculations I'm not sure why you'd store the images - there's a lot of tools that can generate 3D structure images pretty rapidly, so it's probably better to leave that outside the database > Does anyone have any recommendations for the best database software > (e.q. Access or software more directed to chemists)? Or can anyone > recommend a good book on building a chemical database from Access or > the various forms of SQL software. A good book is "Design and Use of Relational Databases in Chemistry" http://www.amazon.com/Design-Use-Relational-Databases-Chemistry/dp/1420064428 ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Got Mole problems? Call Avogadro at 6.02 x 10^23.