From owner-chemistry@ccl.net Mon Oct 30 05:34:00 2006 From: "Jens Thomas j.m.h.thomas###dl.ac.uk" To: CCL Subject: CCL:G: Hyperchem and other "easy" software Message-Id: <-32893-061030053048-6614-0E/fSw9VbnPfRrKuwPUHqw]_[server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 30 Oct 2006 10:29:22 +0000 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas%x%dl.ac.uk] Hi Phil, The CCP1GUI project was started with the intention of doing a lot of the things you've mentioned. It's free (released under the GPL and hosted on Sourceforge) and has (currently relatively simple) tools for building up molecules from scratch, as well as facilities for reading/writing them in a variety of different formats. It can also cope with z-matricies and has facilities to generate these automatically from Carteisan coordinates. There are interfaces (some of them still quite simple) to GAMESS-UK, Dalton, Molpro, ChemShell and MNDO and we are also in the process of adding the ability to submit jobs to computational grids and other remote resources. You can find out more about the CCP1GUI at: http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml The CCP1GUI certainly doesn't fufill all the needs you've mentioned, but I'd hope that it should provide a reasonable framework for adding this sort of functionality. Currently the CCP1GUI is still quite a small project, but as more people participate and provide code to it, it has the potential to expand very quickly. It's written in Python and uses an object-oriented to make it as quick and simple as possible to add new code and build up additional interfaces. Please give it a try and let me know how you get on, and if you have any suggestions. Best wishes, Jens Thomas Phil Hultin hultin++cc.umanitoba.ca wrote: > Sent to CCL by: "Phil Hultin" [hultin _ cc.umanitoba.ca] > This is a multi-part message in MIME format. > > ------=_NextPart_000_011C_01C6F9D3.A1BB2510 > Content-Type: text/plain; > charset="US-ASCII" > Content-Transfer-Encoding: 7bit > > I agree with the statement that Hyperchem's primary advantage is easy use, > and its weakness is in the actual implementation of theoretical models. > > > > If you want a user-friendly interface with good computational tools, Spartan > is probably a better choice and is in the same price range as Hyperchem. > Even so, Spartan is by no means an ideal computational code. > > > > The big problems with MOST computational freeware are 1) poor documentation > and 2) cryptic command line interfaces. While there are very nice freeware > visualization tools (eg Rasmol, Molekel, Molden, SwissView) the range of > tools for creating starting structures for computations is much more > limited, and primarily addresses the peptide and nucleic acid communities > (eg VMD/Molefacture). I have also found that several programs that claim to > be able to save structure files in a given format actually create files that > are not readable by other programs - either because the drawing program uses > a "dialect" of the file format, or the computational program does. Yes, you > can use sometimes use OpenBabel to get around this, but the frustration > factor grows with every step you have to go through to get a usable > structure input file. > > > > There is a need for a simple, reliable and FREE option for general structure > drawing that can save in a variety of formats. The Marvin package from > ChemAxon approaches this goal but it is still not quite what I have in mind. > Such a program would create absolutely canonical 3-D structure files in MOL, > XYZ (simple Cartesian and TINKER formats), PDB (both ATOM and HETATM/CONECT > variants), and unique SMILES. The Dundee PRODRG server on the web can do > this but is not as convenient as a local program on one's own workstation or > PC. > > > > It would also be able to make input files for the common computational > codes: Gaussian, GAMESS, MOPAC. I know that GaussView can do this for > Gaussian but GaussView is not free - in fact it is rather expensive. It is > not essential that this Freeware have all the options for these computations > as buttons or menus, but if it can set up the structure of the file > including the coordinate sets, and then give a command line for the user to > type in the route section etc. that would be very convenient. If it had > some tools for creating z-matrices that would be a nice touch but is not as > important as it once was. > > > > Ok, so I have described what I want for Christmas. Any altruistic > programmers out there? > > > > Dr. Philip G. Hultin > > Professor of Chemistry, > > University of Manitoba > > Winnipeg, MB > > R3T 2N2 > > hultin_._cc.umanitoba.ca > > > http://umanitoba.ca/chemistry/people/hultin > > > > > ------=_NextPart_000_011C_01C6F9D3.A1BB2510 > Content-Type: text/html; > charset="US-ASCII" > Content-Transfer-Encoding: quoted-printable > > xmlns:w=3D"urn:schemas-microsoft-com:office:word" = > xmlns:st1=3D"urn:schemas-microsoft-com:office:smarttags" = > xmlns=3D"http://www.w3.org/TR/REC-html40" > xmlns:ns0=3D"urn:schemas-microsoft-com:office:smarttags"> > > > charset=3Dus-ascii"> > > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"State"/> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"PlaceName"/> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"PlaceType"/> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"City"/> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"place"/> > > > > > > > >
> >

style=3D'font-size:10.0pt; > font-family:Arial'>I agree with the statement that Hyperchem’s = > primary > advantage is easy use, and its weakness is in the actual implementation = > of > theoretical models.

> >

style=3D'font-size:10.0pt; > font-family:Arial'> 

> >

style=3D'font-size:10.0pt; > font-family:Arial'>If you want a user-friendly interface with good > computational tools, Spartan is probably a better choice and is in the = > same > price range as Hyperchem.  Even so, Spartan is by no means an ideal > computational code.

> >

style=3D'font-size:10.0pt; > font-family:Arial'> 

> >

style=3D'font-size:10.0pt; > font-family:Arial'>The big problems with MOST computational freeware are = > 1) > poor documentation and 2) cryptic command line interfaces.  While = > there > are very nice freeware visualization tools (eg Rasmol, Molekel, Molden, > SwissView) the range of tools for creating starting structures for = > computations > is much more limited, and primarily addresses the peptide and nucleic = > acid > communities (eg VMD/Molefacture).  I have also found that several = > programs > that claim to be able to save structure files in a given format actually = > create > files that are not readable by other programs – either because the > drawing program uses a “dialect” of the file format, or the > computational program does.  Yes, you can use sometimes use = > OpenBabel to > get around this, but the frustration factor grows with every step you = > have to > go through to get a usable structure input = > file.

> >

style=3D'font-size:10.0pt; > font-family:Arial'> 

> >

style=3D'font-size:10.0pt; > font-family:Arial'>There is a need for a simple, reliable and FREE = > option for general > structure drawing that can save in a variety of formats.  The = > Marvin > package from ChemAxon approaches this goal but it is still not quite = > what I > have in mind.  Such a program would create absolutely canonical 3-D > structure files in MOL, XYZ (simple Cartesian and TINKER formats), PDB = > (both ATOM > and HETATM/CONECT variants), and unique SMILES.  The Dundee PRODRG = > server > on the web can do this but is not as convenient as a local program on = > one’s > own workstation or PC.

> >

style=3D'font-size:10.0pt; > font-family:Arial'> 

> >

style=3D'font-size:10.0pt; > font-family:Arial'>It would also be able to make input files for the = > common > computational codes: Gaussian, GAMESS, MOPAC.  I know that = > GaussView can > do this for Gaussian but GaussView is not free – in fact it is = > rather > expensive.  It is not essential that this Freeware have all the = > options > for these computations as buttons or menus, but if it can set up the = > structure > of the file including the coordinate sets, and then give a command line = > for the > user to type in the route section etc. that would be very convenient. = >  If > it had some tools for creating z-matrices that would be a nice touch but = > is not > as important as it once was.

> >

style=3D'font-size:10.0pt; > font-family:Arial'> 

> >

style=3D'font-size:10.0pt; > font-family:Arial'>Ok, so I have described what I want for = > Christmas.  Any > altruistic programmers out there?

> >

style=3D'font-size:10.0pt; > font-family:Arial'> 

> >

style=3D'font-size:10.0pt; > font-family:Arial'>Dr. Philip G. Hultin

> >

style=3D'font-size:10.0pt; > font-family:Arial'>Professor of Chemistry,

> >

style=3D'font-size:10.0pt; > font-family:Arial'> w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin" > w:endInsDate=3D"2006-10-27T13:25:00Z"> w:insAuthor=3D"Philip Hultin" > w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin" > w:endInsDate=3D"2006-10-27T13:25:00Z"> w:st=3D"on"> w:st=3D"on">University of = > w:insAuthor=3D"Philip Hultin" w:insDate=3D"2006-10-27T13:25:00Z" > w:endInsAuthor=3D"Philip Hultin" = > w:endInsDate=3D"2006-10-27T13:25:00Z"> = > w:st=3D"on">Manitoba p>

> >

style=3D'font-size:10.0pt; > font-family:Arial'> w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin" > w:endInsDate=3D"2006-10-27T13:25:00Z"> Hultin" > w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin" > w:endInsDate=3D"2006-10-27T13:25:00Z">Winnipeg, w:insAuthor=3D"Philip Hultin" w:insDate=3D"2006-10-27T13:25:00Z" > w:endInsAuthor=3D"Philip Hultin" = > w:endInsDate=3D"2006-10-27T13:25:00Z">MB p>

> >

style=3D'font-size: > 10.0pt;font-family:Arial'>R3T 2N2

> >

style=3D'font-size:10.0pt; > font-family:Arial'> lang=3DFR-CA>hultin_._cc.umanitoba.ca size=3D2 face=3DArial> style=3D'font-size:10.0pt;font-family:Arial'> > >

style=3D'font-size:10.0pt; > font-family:Arial'> href=3D"http://umanitoba.ca/chemistry/people/hultin"> lang=3DFR-CA>http://umanitoba.ca/chemistry/people/hultin >> > > size=3D2 face=3DArial> style=3D'font-size:10.0pt;font-family:Arial'> > >

lang=3DFR-CA > style=3D'font-size:12.0pt'> 

> >
> > > > > > ------=_NextPart_000_011C_01C6F9D3.A1BB2510--> > > > > > From owner-chemistry@ccl.net Mon Oct 30 07:39:00 2006 From: "Patrick Pang skpang===ctimail.com" To: CCL Subject: CCL:G: cannot locate the optimized geometry of Fe(CN)6_(3-) using Gaussian 03 Message-Id: <-32894-061030073732-13304-PSdynCfptnDCkWeF/srY3A/./server.ccl.net> X-Original-From: "Patrick Pang" Date: Mon, 30 Oct 2006 07:37:32 -0500 Sent to CCL by: "Patrick Pang" [skpang,ctimail.com] Dear all, Has anyone experience in performing the geometry optimization of Fe(CN)6_(3-)? I find that the job of the geometry optimization of Fe(CN)6_(4-) is easy but NOT Fe(CN)6_(3-). I use Gaussian 03 to do it, and the input is: P UB98/6-31++G(d,p) Opt=CalcAll SCF=(MaxCycle=2000,NoSymm) Fe(CN)6_3- -3 2 26 0.000000 0.000000 0.000000 6 0.000000 0.000000 2.006685 6 0.000000 2.006685 0.000000 6 0.000000 0.000000 -2.006685 6 0.000000 -2.006685 0.000000 6 2.006685 0.000000 0.000000 6 -2.006685 0.000000 0.000000 7 0.000000 0.000000 3.194174 7 -3.194174 0.000000 0.000000 7 0.000000 0.000000 -3.194174 7 3.194174 0.000000 0.000000 7 0.000000 3.194174 0.000000 7 0.000000 -3.194174 0.000000 The Maximum Force and the RMS Force are never converged, whereas the Maximum Displacement and the RMS Displacement can be coverged in most steps in the geometry optimization, and they can be achieved to coverge in early steps. Has anyone an idea for that? My contact e-mail address is skpang^^ctimail.com Regards Patrick Pang From owner-chemistry@ccl.net Mon Oct 30 10:06:00 2006 From: "Shobe, David David.Shobe*|*sud-chemie.com" To: CCL Subject: CCL:G: cannot locate the optimized geometry of Fe(CN)6_(3-) using Gaussian 03 Message-Id: <-32895-061030100329-1035-3RpsV2yi+fftzOctASjPbg,server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 Oct 2006 16:03:05 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe{:}sud-chemie.com] This may be a sign that Gaussian wants to break the octahedral symmetry. You can try lengthening one of the Fe-CN bonds to break the symmetry and reoptimizing. --David Shobe -----Original Message----- > From: owner-chemistry\a/ccl.net [mailto:owner-chemistry\a/ccl.net] Sent: Monday, October 30, 2006 7:53 AM To: Shobe, David Subject: CCL:G: cannot locate the optimized geometry of Fe(CN)6_(3-) using Gaussian 03 Sent to CCL by: "Patrick Pang" [skpang,ctimail.com] Dear all, Has anyone experience in performing the geometry optimization of Fe(CN)6_(3-)? I find that the job of the geometry optimization of Fe(CN)6_(4-) is easy but NOT Fe(CN)6_(3-). I use Gaussian 03 to do it, and the input is: P UB98/6-31++G(d,p) Opt=CalcAll SCF=(MaxCycle=2000,NoSymm) Fe(CN)6_3- -3 2 26 0.000000 0.000000 0.000000 6 0.000000 0.000000 2.006685 6 0.000000 2.006685 0.000000 6 0.000000 0.000000 -2.006685 6 0.000000 -2.006685 0.000000 6 2.006685 0.000000 0.000000 6 -2.006685 0.000000 0.000000 7 0.000000 0.000000 3.194174 7 -3.194174 0.000000 0.000000 7 0.000000 0.000000 -3.194174 7 3.194174 0.000000 0.000000 7 0.000000 3.194174 0.000000 7 0.000000 -3.194174 0.000000 The Maximum Force and the RMS Force are never converged, whereas the Maximum Displacement and the RMS Displacement can be coverged in most steps in the geometry optimization, and they can be achieved to coverge in early steps. Has anyone an idea for that? My contact e-mail address is skpang!A!ctimail.com Regards Patrick Panghttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Mon Oct 30 10:40:00 2006 From: "William F. Polik polik-*-hope.edu" To: CCL Subject: CCL:G: Hyperchem and other "easy" software Message-Id: <-32896-061028224640-9532-eIMTeDLoMEiaNiKKd2vATw^^server.ccl.net> X-Original-From: "William F. Polik" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Sat, 28 Oct 2006 21:58:11 -0400 Mime-Version: 1.0 Sent to CCL by: "William F. Polik" [polik/./hope.edu] At 04:42 PM 10/27/2006, Phil Hultin hultin++cc.umanitoba.ca wrote: >It would also be able to make input files for the common computational >codes: Gaussian, GAMESS, MOPAC. I know that GaussView can do this for >Gaussian but GaussView is not free - in fact it is rather expensive. It is >not essential that this Freeware have all the options for these computations >as buttons or menus, but if it can set up the structure of the file >including the coordinate sets, and then give a command line for the user to >type in the route section etc. that would be very convenient. If it had >some tools for creating z-matrices that would be a nice touch but is not as >important as it once was. It sounds like you are describing WebMO http://www.webmo.net which is a web-based interface to various computational chemistry programs (Gamess, Gaussian, Molpro, Mopac, Nwchem, Qchem, Tinker). WebMO installs on the same unix machine as your computational chemistry program(s). After logging in, users draw their molecule using a 3-D editor, select the program and type of calculation, and submit the job. When the job completes, the results are parsed and displayed in 3-D graphical and tabular form on a web page. For more advanced users, the input file (including route section and z-matrix) is available and editable, and the complete output file is available. Best yet, since WebMO is a web-based product, you can try it out without actually installing it on your machine! Just visit the WebMO Working Demo at http://www.webmo.net/demo and try it out. >Ok, so I have described what I want for Christmas. Any altruistic >programmers out there? WebMO is free. Merry Christmas! Will Polik ================================ Dr. William F. Polik Hofma Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik!=!hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ================================ From owner-chemistry@ccl.net Mon Oct 30 11:31:00 2006 From: "Dimitrios A Pantazis pantazis/a\hotmail.com" To: CCL Subject: CCL:G: cannot locate the optimized geometry of Fe(CN)6_(3-) Message-Id: <-32897-061030112821-18496-pxs5hUKtYdTk6KoZ1H85lQ.@.server.ccl.net> X-Original-From: "Dimitrios A Pantazis" Date: Mon, 30 Oct 2006 11:28:21 -0500 Sent to CCL by: "Dimitrios A Pantazis" [pantazis:+:hotmail.com] Hi Patrick, a low-spin Fe(CN)6_(3-) complex would be "(t2g)5" and thus it has a distorted octahedral structure. If you start the calculation assuming Oh point group, then Gaussian will not be able to move away from the octahedral symmetry, hence the convergence problem. Dimitrios From owner-chemistry@ccl.net Mon Oct 30 12:05:00 2006 From: "Soren Eustis soren::jhu.edu" To: CCL Subject: CCL:G: cannot locate the optimized geometry of Fe(CN)6_(3-) using Gaussian 03 Message-Id: <-32898-061030110343-16556-hn6Mm5GcMEgzcs3TqPSQBQ*server.ccl.net> X-Original-From: "Soren Eustis" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Mon, 30 Oct 2006 11:03:34 -0500 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren%x%jhu.edu] I have had problems with G03 converging when analyzing systems with very flat potentials. When I have an oscillating energy that leads to a failure to converge, I restart with the keywords Opt=(Newton, NRScale). This makes sure that each move is not too large and it uses the Newton-Raphson method during the optimization. It has seemed to work well for me. Soren N. Eustis Graduate Research Assistant Department of Chemistry Johns Hopkins University Remsen Hall 3400 N Charles Street Baltimore, MD 21218 (410) 516-4675 (office) (410) 925-5167 (cell) (410) 516-8420 (fax) soren|-|jhu.edu -----Original Message----- > From: owner-chemistry|-|ccl.net [mailto:owner-chemistry|-|ccl.net] Sent: Monday, October 30, 2006 10:37 AM To: Eustis, Soren Subject: CCL:G: cannot locate the optimized geometry of Fe(CN)6_(3-) using Gaussian 03 Sent to CCL by: "Shobe, David" [David.Shobe{:}sud-chemie.com] This may be a sign that Gaussian wants to break the octahedral symmetry. You can try lengthening one of the Fe-CN bonds to break the symmetry and reoptimizing. --David Shobe -----Original Message----- > From: owner-chemistry]![ccl.net [mailto:owner-chemistry]![ccl.net] Sent: Monday, October 30, 2006 7:53 AM To: Shobe, David Subject: CCL:G: cannot locate the optimized geometry of Fe(CN)6_(3-) using Gaussian 03 Sent to CCL by: "Patrick Pang" [skpang,ctimail.com] Dear all, Has anyone experience in performing the geometry optimization of Fe(CN)6_(3-)? I find that the job of the geometry optimization of Fe(CN)6_(4-) is easy but NOT Fe(CN)6_(3-). I use Gaussian 03 to do it, and the input is: P UB98/6-31++G(d,p) Opt=CalcAll SCF=(MaxCycle=2000,NoSymm) Fe(CN)6_3- -3 2 26 0.000000 0.000000 0.000000 6 0.000000 0.000000 2.006685 6 0.000000 2.006685 0.000000 6 0.000000 0.000000 -2.006685 6 0.000000 -2.006685 0.000000 6 2.006685 0.000000 0.000000 6 -2.006685 0.000000 0.000000 7 0.000000 0.000000 3.194174 7 -3.194174 0.000000 0.000000 7 0.000000 0.000000 -3.194174 7 3.194174 0.000000 0.000000 7 0.000000 3.194174 0.000000 7 0.000000 -3.194174 0.000000 The Maximum Force and the RMS Force are never converged, whereas the Maximum Displacement and the RMS Displacement can be coverged in most steps in the geometry optimization, and they can be achieved to coverge in early steps. Has anyone an idea for that? My contact e-mail address is skpang!A!ctimail.com Regards Patrick Panghttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemis try/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Oct 30 13:12:01 2006 From: "Shobe, David David.Shobe+*+sud-chemie.com" To: CCL Subject: CCL:G: cannot locate the optimized geometry of Fe(CN)6_(3-) using Gaussian 03 Message-Id: <-32899-061030131018-31325-xbItW1+VDHdwJx0tg2R2Lg:_:server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 Oct 2006 19:09:59 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe]*[sud-chemie.com] I just thought of something. Are these ions really stable by themselves (no counterions), in the gas phase? Maybe Patrick will try my advice and the loosened CN- will shoot away like a cannonball! :-) --David Shobe -----Original Message----- > From: owner-chemistry(~)ccl.net [mailto:owner-chemistry(~)ccl.net] Sent: Monday, October 30, 2006 12:10 PM To: Shobe, David Subject: CCL:G: cannot locate the optimized geometry of Fe(CN)6_(3-) using Gaussian 03 Sent to CCL by: "Soren Eustis" [soren%x%jhu.edu] I have had problems with G03 converging when analyzing systems with very flat potentials. When I have an oscillating energy that leads to a failure to converge, I restart with the keywords Opt=(Newton, NRScale). This makes sure that each move is not too large and it uses the Newton-Raphson method during the optimization. It has seemed to work well for me. Soren N. Eustis Graduate Research Assistant Department of Chemistry Johns Hopkins University Remsen Hall 3400 N Charles Street Baltimore, MD 21218 (410) 516-4675 (office) (410) 925-5167 (cell) (410) 516-8420 (fax) soren%%jhu.edu -----Original Message----- > From: owner-chemistry%%ccl.net [mailto:owner-chemistry%%ccl.net] Sent: Monday, October 30, 2006 10:37 AM To: Eustis, Soren Subject: CCL:G: cannot locate the optimized geometry of Fe(CN)6_(3-) using Gaussian 03 Sent to CCL by: "Shobe, David" [David.Shobe{:}sud-chemie.com] This may be a sign that Gaussian wants to break the octahedral symmetry. You can try lengthening one of the Fe-CN bonds to break the symmetry and reoptimizing. --David Shobe -----Original Message----- > From: owner-chemistry]![ccl.net [mailto:owner-chemistry]![ccl.net] Sent: Monday, October 30, 2006 7:53 AM To: Shobe, David Subject: CCL:G: cannot locate the optimized geometry of Fe(CN)6_(3-) using Gaussian 03 Sent to CCL by: "Patrick Pang" [skpang,ctimail.com] Dear all, Has anyone experience in performing the geometry optimization of Fe(CN)6_(3-)? I find that the job of the geometry optimization of Fe(CN)6_(4-) is easy but NOT Fe(CN)6_(3-). I use Gaussian 03 to do it, and the input is: P UB98/6-31++G(d,p) Opt=CalcAll SCF=(MaxCycle=2000,NoSymm) Fe(CN)6_3- -3 2 26 0.000000 0.000000 0.000000 6 0.000000 0.000000 2.006685 6 0.000000 2.006685 0.000000 6 0.000000 0.000000 -2.006685 6 0.000000 -2.006685 0.000000 6 2.006685 0.000000 0.000000 6 -2.006685 0.000000 0.000000 7 0.000000 0.000000 3.194174 7 -3.194174 0.000000 0.000000 7 0.000000 0.000000 -3.194174 7 3.194174 0.000000 0.000000 7 0.000000 3.194174 0.000000 7 0.000000 -3.194174 0.000000 The Maximum Force and the RMS Force are never converged, whereas the Maximum Displacement and the RMS Displacement can be coverged in most steps in the geometry optimization, and they can be achieved to coverge in early steps. Has anyone an idea for that? My contact e-mail address is skpang!A!ctimail.com Regards Patrick Panghttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/ch emis try/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/ch emistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Mon Oct 30 13:47:01 2006 From: "SANDEEP KUMAR kumarsan(_)jhu.edu" To: CCL Subject: CCL:G: Hyperchem and other "easy" software Message-Id: <-32900-061030123025-28370-tvgWYgaXviiiv2ZuBR7q7g _ server.ccl.net> X-Original-From: SANDEEP KUMAR Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Mon, 30 Oct 2006 11:30:13 -0500 MIME-version: 1.0 Sent to CCL by: SANDEEP KUMAR [kumarsan(-)jhu.edu] Prof. Polik: Thanks for describing WebMO. I appears nice. I was wondering if there is a similar web-based free server which could also do virtual screening. Sincerely, Sandeep Kumar ------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan]-[jhu.edu. URL: https://jshare.johnshopkins.edu/skumar23/public_html/ Previous URL: http://www.lecb.ncifcrf.gov/~kumarsan ----- Original Message ----- > From: "William F. Polik polik-*-hope.edu" Date: Monday, October 30, 2006 10:48 am Subject: CCL:G: Hyperchem and other "easy" software To: "Kumar, Sandeep " > Sent to CCL by: "William F. Polik" [polik/./hope.edu] > > At 04:42 PM 10/27/2006, Phil Hultin hultin++cc.umanitoba.ca wrote: > >It would also be able to make input files for the common computational > >codes: Gaussian, GAMESS, MOPAC. I know that GaussView can do this for > >Gaussian but GaussView is not free - in fact it is rather expensive. > It is > >not essential that this Freeware have all the options for these computations > >as buttons or menus, but if it can set up the structure of the file > >including the coordinate sets, and then give a command line for the > user to > >type in the route section etc. that would be very convenient. If it > had > >some tools for creating z-matrices that would be a nice touch but is > not as > >important as it once was. > > It sounds like you are describing WebMO > > which is a web-based interface to various computational chemistry > programs (Gamess, Gaussian, Molpro, Mopac, Nwchem, Qchem, Tinker). > > WebMO installs on the same unix machine as your computational > chemistry program(s). After logging in, users draw their molecule > using a 3-D editor, select the program and type of calculation, and > submit the job. When the job completes, the results are parsed and > displayed in 3-D graphical and tabular form on a web page. For more > advanced users, the input file (including route section and z-matrix) > > is available and editable, and the complete output file is available. > > Best yet, since WebMO is a web-based product, you can try it out > without actually installing it on your machine! Just visit the WebMO > > Working Demo at > > and try it out. > > >Ok, so I have described what I want for Christmas. Any altruistic > >programmers out there? > > WebMO is free. Merry Christmas! > > Will Polik > > > ================================ > Dr. William F. Polik > Hofma Professor of Chemistry > > Department of Chemistry > Hope College > 35 East 12th Street > Holland, MI 49422-9000 > USA > > polik[]hope.edu > > tel: (616) 395-7639 > fax: (616) 395-7118 > ================================> > > Before posting, check wait time at: > > Job: > Conferences: > > Search Messages: (login: ccl, Password: search)> > > RTFI:> From owner-chemistry@ccl.net Mon Oct 30 15:00:00 2006 From: "Ana Vila Verde avilaverde-.-fisica.uminho.pt" To: CCL Subject: CCL: About Rosetta-protein structure prediction program Message-Id: <-32901-061030135717-8610-j4/kCW3ZZPy7I9aAJqu87w(a)server.ccl.net> X-Original-From: "Ana Vila Verde" Date: Mon, 30 Oct 2006 13:57:16 -0500 Sent to CCL by: "Ana Vila Verde" [avilaverde^fisica.uminho.pt] Hello all, I am trying to run Rosetta in a local cluster, but I haven't been able to make it go. Some example error messages are below my signature. I was wondering if there are users out there who have experienced similar difficulties and who may be able to help me. I've searched everywhere I can think of and I am absolutely stuck. Thanks, Ana 1) This message was obtained trying to run the example script in the "rosetta/RosettaAbinitio/examples" directory. In principle it should work with no glitches, but it doesn't. ROSETTA WARNING - cannot open /usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z.out to get silent mode file format ROSETTA WARNING - cannot unlink(/usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z.last_pdb): No such file or directory Cleaning rosetta out file: /usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z.out Creating cleaned out file: /usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z_clean.out Creating corrupted out file: /usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z_dirty.out ROSETTA ERROR - Can't open file /usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z.out: No such file or directory ___________________________________________________________________________ 2) I was able to run the example in /usr/global/rosetta/RosettaFragments/examples, but when I try to run my own sequence to get a fragment library (input is the fasta sequence, a file that I got from jufo and another that I got from psipred), I get this error message: ... setup 60 ./status.200_v1_3_aa6NGB seq_weight: 1. ss_weight: 0.5 chsft_weight: 0.449999988 weight_proline_phi 0.434294462 input_pdb 11./6NGB.pdb input_pdb 11./6NGB.pdb input checkpoint 11./6NGB_.checkpoint protein_name, chain6NGB read_phd 16./6NGB_.phd No file in path read_jones 16./6NGB_.psipred_ss2 read_jones 16 ./6NGB_.jones read_jones 16 ./6NGB_.psipred read_jufo 16./6NGB_.jufo_ss reading rdb file./6NGB_.rdb no rdb file read_rdb 16./6NGB_.rdb NNMAKE FAILED: no valid secondary structure predictions found nnmake failed From owner-chemistry@ccl.net Mon Oct 30 16:39:00 2006 From: "Gustavo Seabra gustavo.seabra_+_gmail.com" To: CCL Subject: CCL:G: GO3 W vs GO3 Linux Message-Id: <-32902-061030163334-13579-7CaH/yRsdgnKq6QnqStO9A*server.ccl.net> X-Original-From: "Gustavo Seabra" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 30 Oct 2006 16:33:27 -0500 MIME-Version: 1.0 Sent to CCL by: "Gustavo Seabra" [gustavo.seabra**gmail.com] Definetely, the linux version will be faster. (I'm yet to hear about a scientific application that runs faster in Windows.;-) Also, there was a problem with the windows version being unable to generate the orbitals, which I don't know if it has been solved. HTH. Gustavo. On 10/29/06, neeraj misra misraneeraj|,|gmail.com wrote: > Sent to CCL by: "neeraj misra" [misraneeraj%a%gmail.com] > > DEAR CCL'ERS > I WOULD BE GRATEFUL IF SOMEONE COULD TELL ME WHICH ONE WOULD BE FASTER/BETTER ON COMPARISON. > > GAUSSIAN 03 FOR WINDOWS VERSUS GAUSSIAN 03 FOR LINUX. > IS A CALCULATION ON AS LINUX PLATEFORM FASTER. > THANKS IN ADVANCE From owner-chemistry@ccl.net Mon Oct 30 17:14:00 2006 From: "Szabolcs Csepregi scsepregi%a%chemaxon.com" To: CCL Subject: CCL: Information on Reaction Similarity Searching Message-Id: <-32903-061030170420-994-w7cKBpxAa3daA/RbQ5k0ow.@.server.ccl.net> X-Original-From: Szabolcs Csepregi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 30 Oct 2006 23:04:10 +0100 MIME-Version: 1.0 Sent to CCL by: Szabolcs Csepregi [scsepregi%x%chemaxon.com] Hi Scott, See this link about how this is done in JChem: http://www.chemaxon.com/jchem/doc/user/RFp.html I hope this helps, Szabolcs Szabolcs Csepregi, PhD Director of Search Technologies, ChemAxon Ltd. http://www.chemaxon.com Skype: szabolcs.csepregi Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 Scott G Flicker sflicker2#%#earthlink.net wrote: > Sent to CCL by: "Scott G Flicker" [sflicker2[A]earthlink.net] > I am looking for information on algorithms to conduct Reaction Similarity Searches against a chemical structure & reaction database. I have control over the database so I could add indexes etc if necessary. > > Thanks> > > > > From owner-chemistry@ccl.net Mon Oct 30 19:42:00 2006 From: "Cen Gao cgao(_)mail.rochester.edu" To: CCL Subject: CCL: About Rosetta-protein structure prediction program Message-Id: <-32904-061030183136-23793-FwdrtLePqUReKlolx/TTcA .. server.ccl.net> X-Original-From: Cen Gao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 30 Oct 2006 18:31:24 -0500 MIME-Version: 1.0 Sent to CCL by: Cen Gao [cgao]~[mail.rochester.edu] Hi Ana I guess you might not have rosetta & its affiliated program installed properly. To test rosetta try to go to RosettaAbinitio/examples/1d3z/ and run ROSETTA -fasta 1d3z_.fasta -nstruct 1 -verbose (replace ROSETTA with your own binary) to see if it works. I guess the first error is because there is not aa1d3z.out file in examples/test/ , the default directory is examples/1d3z/ ,try to edit paths.txt to point to the right aa1d3z.out file and you will be fine. for the second error,can you show me more of your input and output. My feeling is that it is still the directory problem (maybe SAM is not properly installed, and you didn't specified -nosam in command-line) or you didn't specified the filename of your psipred&jufo file correctly. But I am not so sure. Cen -- Cen Gao Hutchinson Room 426 Department of Chemistry, Box 270216 University of Rochester Rochester, New York 14627-0216 Ana Vila Verde avilaverde-.-fisica.uminho.pt wrote: > Sent to CCL by: "Ana Vila Verde" [avilaverde^fisica.uminho.pt] > Hello all, > > I am trying to run Rosetta in a local cluster, but I haven't been able to make it go. Some example error messages are below my signature. I was wondering if there are users out there who have experienced similar difficulties and who may be able to help me. I've searched everywhere I can think of and I am absolutely stuck. > > Thanks, > > Ana > > 1) This message was obtained trying to run the example script in the "rosetta/RosettaAbinitio/examples" directory. In principle it should work with no glitches, but it doesn't. > > ROSETTA WARNING - cannot open /usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z.out to get silent mode file format > ROSETTA WARNING - cannot unlink(/usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z.last_pdb): No such file or directory > Cleaning rosetta out file: /usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z.out > Creating cleaned out file: /usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z_clean.out > Creating corrupted out file: /usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z_dirty.out > ROSETTA ERROR - Can't open file /usr/global/rosetta-2.1.0/RosettaAbinitio/examples/test/./aa1d3z.out: No such file or directory > > ___________________________________________________________________________ > > 2) I was able to run the example in /usr/global/rosetta/RosettaFragments/examples, but when I try to run my own sequence to get a fragment library (input is the fasta sequence, a file that I got from jufo and another that I got from psipred), I get this error message: > > ... > setup 60 ./status.200_v1_3_aa6NGB > seq_weight: 1. > ss_weight: 0.5 > chsft_weight: 0.449999988 > weight_proline_phi 0.434294462 > input_pdb 11./6NGB.pdb > input_pdb 11./6NGB.pdb > input checkpoint 11./6NGB_.checkpoint > protein_name, chain6NGB > read_phd 16./6NGB_.phd > No file in path > read_jones 16./6NGB_.psipred_ss2 > read_jones 16 ./6NGB_.jones > read_jones 16 ./6NGB_.psipred > read_jufo 16./6NGB_.jufo_ss > reading rdb file./6NGB_.rdb > no rdb file > read_rdb 16./6NGB_.rdb > NNMAKE FAILED: no valid secondary structure predictions found > nnmake failed> > > > > > From owner-chemistry@ccl.net Mon Oct 30 21:33:00 2006 From: "jun tie cheng ccl]=[mail.sioc.ac.cn" To: CCL Subject: CCL: theoretical study of pi-pi stacking Message-Id: <-32905-061030213021-23540-1J0ATu9zCQCMGWp+EdaQ+g*o*server.ccl.net> X-Original-From: "jun tie cheng" Date: Mon, 30 Oct 2006 21:30:21 -0500 Sent to CCL by: "jun tie cheng" [ccl++mail.sioc.ac.cn] Hi all, Can anyone suggest some articles on the theoretical study of pi-pi stacking? thanks in advance! sincerely, JAY