From owner-chemistry@ccl.net Wed Sep 22 01:09:00 2010 From: "Michael K. Gilson mgilson.:.ucsd.edu" To: CCL Subject: CCL: Protein-ligand test sets Message-Id: <-42801-100921235854-14447-L5MbiNvLYfx2kp/G8NBI0Q^^^server.ccl.net> X-Original-From: "Michael K. Gilson" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 21 Sep 2010 20:58:20 -0700 MIME-Version: 1.0 Sent to CCL by: "Michael K. Gilson" [mgilson[A]ucsd.edu] Dear Colleagues, BindingDB has begun working on extracting protein-ligand binding datasets suitable for parameterizing or testing protein-ligand modeling codes. Each set has roughly 10-50 congeneric small molecules with a range of affinities for a single protein target. There is at least one protein-ligand structure from the series in the PDB. Each dataset is freely downloadable in the form of an SDfile. The following page summarizes the first 15 datasets, including links for the downloads. The "View Compounds" link at the end of each row provides a view of the compounds in the series. http://www.bindingdb.org/validation_sets/index.jsp We hope some of you will find these useful, and we would welcome comments and suggestions. Best regards, Mike -- Michael K. Gilson, M.D., Ph.D. Professor Skaggs School of Pharm. and Pharm. Sci. University of California San Diego 9500 Gilman Drive, MC 0736 La Jolla, California, 92093-0736 Office: 858-822-0622 http://pharmacy.ucsd.edu/faculty/Gilson.shtml From owner-chemistry@ccl.net Wed Sep 22 04:40:00 2010 From: "SUBHADEEP SAHA saha.subhadeep===gmail.com" To: CCL Subject: CCL: optimization of an particular atom with different basis set Message-Id: <-42802-100922030906-24909-2BZu1+asIyv/G9iU9IfMUQ~~server.ccl.net> X-Original-From: SUBHADEEP SAHA Content-Type: multipart/alternative; boundary=0015175cb896d5063a0490d3d1b1 Date: Wed, 22 Sep 2010 12:38:59 +0530 MIME-Version: 1.0 Sent to CCL by: SUBHADEEP SAHA [saha.subhadeep^^gmail.com] --0015175cb896d5063a0490d3d1b1 Content-Type: text/plain; charset=ISO-8859-1 Dear all, I have optimized a Cu-complex with 6-31g basis set.Now if I want to optimize only the Cu atom with a bigger basis set what should I write in the input line?Can any one plz help me out? Thanks in advance.... Regards, Subhadeep Saha C/O Dr.Rahul Banerjee Materials and Physical Chemistry Division National Chemical Laboratory Dr. Homi Bhabha Road Pune:411008 Maharasthra India Ph:+91-20-2590-2387 +91-20-2590-2535 +91-20-2590-2598 --0015175cb896d5063a0490d3d1b1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear all,

I have optimized a Cu-complex with 6-31g basis= set.Now if I want to optimize only the Cu atom with a bigger basis set wha= t should I write in the input line?Can any one plz help me out?

Thanks in advance....

=A0
Regard= s,
Subhadeep Saha
C/O Dr.Rahul Banerjee
Materials and Physical Che= mistry Division
National Chemical Laboratory
Dr. Homi Bhabha Road
Pune:411008
Maharasthra
India
Ph:+91-20-2590-2387
=A0 =A0=A0 +9= 1-20-2590-2535
=A0 =A0=A0 +91-20-2590-2598
--0015175cb896d5063a0490d3d1b1-- From owner-chemistry@ccl.net Wed Sep 22 05:14:00 2010 From: "Sagarika Dev sagarika.dev ~~ gmail.com" To: CCL Subject: CCL: Td-DFT: Transition dipole moment Message-Id: <-42803-100922045002-9142-zCTCqVYMGPaZZF/ziC+zSg-$-server.ccl.net> X-Original-From: "Sagarika Dev" Date: Wed, 22 Sep 2010 04:50:00 -0400 Sent to CCL by: "Sagarika Dev" [sagarika.dev]~[gmail.com] Dear All, I have some doubt on TD-DFT calculation. I was trying to calculate transition dipole moment for some molecule. My questions are 1. I am getting Transition electric dipole moments for different excited states in X,Y and Z componets. How can I visualise the the vector (any visualisation software that will generate the vector along with the atom coordiantes?) 2. how can I convert the Z-polarisation in terms of degree (as this may give information of charge transfer between the orbitals (reference: J.M.Jean and K.B.Hall, PNAS 2001 vol.98, no.1, 37-41)? May I use NBO for finding out the charge transfer phenomena? thanks in advance Sagarika From owner-chemistry@ccl.net Wed Sep 22 08:11:00 2010 From: "allouche#%#lasim.univ-lyon1.fr" To: CCL Subject: CCL: Td-DFT: Transition dipole moment Message-Id: <-42804-100922073034-8814-djpA+acKU4skj8alUb10wA]=[server.ccl.net> X-Original-From: allouche,+,lasim.univ-lyon1.fr Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 22 Sep 2010 13:30:27 +0200 MIME-Version: 1.0 Sent to CCL by: allouche.:.lasim.univ-lyon1.fr Dear Sagarika, Gabedit can visualise the vector : From the popup menu, select set/dipole . You can download gabedit from gabedit.sourceforge.net. Best regards, > > Sent to CCL by: "Sagarika Dev" [sagarika.dev]~[gmail.com] > Dear All, > I have some doubt on TD-DFT calculation. I was trying to calculate > transition dipole moment for some molecule. My questions are > > 1. I am getting Transition electric dipole moments for different excited > states in X,Y and Z componets. How can I visualise the the vector (any > visualisation software that will generate the vector along with the atom > coordiantes?) > > 2. how can I convert the Z-polarisation in terms of degree (as this may give > information of charge transfer between the orbitals (reference: J.M.Jean and > K.B.Hall, PNAS 2001 vol.98, no.1, 37-41)? > > May I use NBO for finding out the charge transfer phenomena? > > thanks in advance > Sagarika> > > -------------------------------------------------------------------------- Ce message a été envoyé depuis le webmail IMP (Internet Messaging Program) From owner-chemistry@ccl.net Wed Sep 22 08:45:00 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= uekstrom#,#gmail.com" To: CCL Subject: CCL:G: optimization of an particular atom with different basis set Message-Id: <-42805-100922052302-14163-FEyjc+/TggjDV3qDFEtT0Q!^!server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 22 Sep 2010 11:22:54 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [uekstrom\a/gmail.com] On Wed, Sep 22, 2010 at 9:08 AM, SUBHADEEP SAHA saha.subhadeep===gmail.com wrote: > Dear all, > I have optimized a Cu-complex with 6-31g basis set.Now if I want to optimize > only the Cu atom with a bigger basis set what should I write in the input > line?Can any one plz help me out? > Thanks in advance.... Maybe plz contact the company that made the software you are using? I understand it's more convenient for you to ask here instead of asking someone in your lab, or going to http://gaussian.com/g_tech/g_ur/k_gen.htm and read the answer. However, if you are paying for software you should also demand help from the same place, and not rely on the community to provide support for free. Otherwise the software companies will never improve the usability of their software. Sincerely, Dr Ulf Ekström From owner-chemistry@ccl.net Wed Sep 22 10:51:00 2010 From: "Reynier Suard az reynier.suardiaz(a)gmail.com" To: CCL Subject: CCL:G: freezen dihedrals in five-membered rings Message-Id: <-42806-100922104948-6972-tcLXl69FSuu0sw9l+6dd8A(~)server.ccl.net> X-Original-From: "Reynier Suard az" Date: Wed, 22 Sep 2010 10:49:47 -0400 Sent to CCL by: "Reynier Suard az" [reynier.suardiaz]_[gmail.com] Dear All I want to generate a lot of conformations of furanose ring (or cyclopentane?) and later partially optimize them but keeping frozen the dihedral angles. I am trying to use redundant coordinates in gaussian writing at the end of the input gaussian file the desired dihedrals to keep frozen. I am receiving an error message when i try to keep frozen more than two dihedral angles (of the ring) at the same time. For example if I try to froze the five dihedrals of the ring I get the following message: ------ Iteration 99 RMS(Cart)= 0.00001156 RMS(Int)= 0.00309967 Iteration100 RMS(Cart)= 0.00001134 RMS(Int)= 0.00310385 New curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in C:\G03W\l101.exe at Mon Sep 20 17:48:17 2010. Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 7 Scr= 1 --------- I receive this error message even when I try to freeze the dihedral at the same value they already have in the initial structure. Is not possible what am I trying to do? How can I overcome this problem with gaussian? Is there any other possibility to do this kind of partial optimization in five-membered rings? Note that I can not freeze all the dihedrals using optimization in internal coordinates (opt=z-matrix with a separate input section of "constants") because of to define a z-matrix of a five-membered ring are necesary only two dihedrals, so I have to use redundants. any comments or sugestions would be appreciatte thanks in advance and very best regards Reynier From owner-chemistry@ccl.net Wed Sep 22 14:13:00 2010 From: "Close, David M. CLOSED~!~mail.etsu.edu" To: CCL Subject: CCL:G: freezen dihedrals in five-membered rings Message-Id: <-42807-100922141020-9745-1lXP93zWATjWcqWbiIZ5WA++server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 22 Sep 2010 18:09:44 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED#,#mail.etsu.edu] Reynier: There is no limit to how many dihedrals you can freeze. The problem is that you typed something wrong. Notice that the program tried 99 iterations to fit you frozen coordiate information into the optimization routine. Either you connected the coordinates incorrectly, or did not have enough precision in the frozen coordinate. So if the input line has something like 10 5 6 8 31.3, first look at the string 10 5 6 8 and make sure this is correct. The use a graphics program to examine the actual dihedral geometry. Run through the 4 atoms in the string 10 5 6 8 and see what the graphic program thinks the dihedral angle actually is. Copy the value to 5-6 decimal places and re enter the data. If this doesn't work, then you have to use trial and error. You said that freezing 2 dihedrals works. But how many iterations did it take? I would expect only 2-3. If more, then refine the coordinates, and then add a third frozen dihedral. You can quickly find the offending entry when the optimization routine bombs. Regards, Dave Close. ________________________________________ > From: owner-chemistry+closed==etsu.edu:-:ccl.net [owner-chemistry+closed==etsu.edu:-:ccl.net] on behalf of Reynier Suard az reynier.suardiaz(a)gmail.com [owner-chemistry:-:ccl.net] Sent: Wednesday, September 22, 2010 10:49 AM To: Close, David M. Subject: CCL:G: freezen dihedrals in five-membered rings Sent to CCL by: "Reynier Suard az" [reynier.suardiaz]_[gmail.com] Dear All I want to generate a lot of conformations of furanose ring (or cyclopentane?) and later partially optimize them but keeping frozen the dihedral angles. I am trying to use redundant coordinates in gaussian writing at the end of the input gaussian file the desired dihedrals to keep frozen. I am receiving an error message when i try to keep frozen more than two dihedral angles (of the ring) at the same time. For example if I try to froze the five dihedrals of the ring I get the following message: ------ Iteration 99 RMS(Cart)= 0.00001156 RMS(Int)= 0.00309967 Iteration100 RMS(Cart)= 0.00001134 RMS(Int)= 0.00310385 New curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in C:\G03W\l101.exe at Mon Sep 20 17:48:17 2010. Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 7 Scr= 1 --------- I receive this error message even when I try to freeze the dihedral at the same value they already have in the initial structure. Is not possible what am I trying to do? How can I overcome this problem with gaussian? Is there any other possibility to do this kind of partial optimization in five-membered rings? Note that I can not freeze all the dihedrals using optimization in internal coordinates (opt=z-matrix with a separate input section of "constants") because of to define a z-matrix of a five-membered ring are necesary only two dihedrals, so I have to use redundants. any comments or sugestions would be appreciatte thanks in advance and very best regards Reynierhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt