From owner-chemistry@ccl.net Tue Apr 22 00:20:01 2008 From: "Rajarshi Guha rguha(a)indiana.edu" To: CCL Subject: CCL: How to implement your own Daylight or MACCS fingerprint? Message-Id: <-36804-080422001721-17319-PXHWgyUKY9SxSf4Ti5LbFw:-:server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 22 Apr 2008 00:17:06 -0400 Mime-Version: 1.0 (Apple Message framework v753) Sent to CCL by: Rajarshi Guha [rguha[]indiana.edu] -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Apr 21, 2008, at 10:36 PM, Tiejun Cheng tjcheng.:.mail.sioc.ac.cn wrote: > > Sent to CCL by: "Tiejun Cheng" [tjcheng:_:mail.sioc.ac.cn] > Hi all, > > Anyone know or any clue on how to implement the Daylight or MACCS > fingerprint? These two are very useful. You can take a look at http://www.mdl.com/solutions/white_papers/ SSKeys_whitepaper.jsp which describes the features encoded by the MACCS keys - I'm not sure whether it explicitly decsribes the 166 keys or whether. Given the features you can define SMARTS for them and create a fingerprint. However some of the definitions can be vague - ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- All theoretical chemistry is really physics; and all theoretical chemists know it. -- Richard P. Feynman -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkgNZsMACgkQZqGSLFHnnoS1TwCcCSChReQjAJtk/3wx2qEiB43E l8gAn3o6zLb/BsVAdFLmvYpdXZBLVQoL =VALQ -----END PGP SIGNATURE----- From owner-chemistry@ccl.net Tue Apr 22 04:24:01 2008 From: "Lukasz Cwiklik cwiklik{:}gmail.com" To: CCL Subject: CCL: Helps on Molecular Dynamics Message-Id: <-36805-080422042233-4330-TL7fmqAOlz/iGNJ0A+nVDw-x-server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 22 Apr 2008 11:22:14 +0300 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik+/-gmail.com] On Tue, Apr 22, 2008 at 5:51 AM, Ariza Ahmad nriza- -hotmail.com wrote: > > Sent to CCL by: "Ariza Ahmad" [nriza^_^hotmail.com] > Hi All, > I am new to Molecular Dynamic simulations. > Actually I'm using Fortran in Linux for the simulations > Now I need to find an MD software for Windows XP operating system > Is there any? I found Gromacs which I think can be installed on both Linux and Windows system.But I dont know how to install in Windows. Could anyone please help me..or giving some ideas? Dear Ahmad, Gromacs is definitely the software worth trying. I do not have experience with Gromacs and Windows, but there is a binary version of Gromacs 3.2.1 for Windows, contributed by Peiquan Chen from China. In order to install this you just need a cpp compiler and its location set in mdp file. The package can be downloaded from: http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,48/Itemid,26/ And of course, you can always compile Gromacs under Windows from the source code. By the way, personally I suggest to use Gromacs with Linux. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Tue Apr 22 05:31:01 2008 From: "Chris Howard c.k.howard\a/reading.ac.uk" To: CCL Subject: CCL: Helps on Molecular Dynamics Message-Id: <-36806-080422052919-1400-NCClskVcKmBrfACOX/VCYA:+:server.ccl.net> X-Original-From: "Chris Howard" Content-Language: en-gb Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 22 Apr 2008 09:45:58 +0100 MIME-Version: 1.0 Sent to CCL by: "Chris Howard" [c.k.howard:+:reading.ac.uk] Hi Ahmed, I would strongly recommend the DL_POLY suite - it's free for academic use and is an incredibly powerful MD application. It can be run in windows - or much preferably, in windows using a CYGWIN shell (which is a very powerful tool anyway). All the best, Chris -----Original Message----- > From: owner-chemistry:-:ccl.net [mailto:owner-chemistry:-:ccl.net] Sent: 22 April 2008 09:22 To: Howard, Chris Subject: CCL: Helps on Molecular Dynamics Sent to CCL by: "Lukasz Cwiklik" [cwiklik+/-gmail.com] On Tue, Apr 22, 2008 at 5:51 AM, Ariza Ahmad nriza- -hotmail.com wrote: > > Sent to CCL by: "Ariza Ahmad" [nriza^_^hotmail.com] > Hi All, > I am new to Molecular Dynamic simulations. > Actually I'm using Fortran in Linux for the simulations > Now I need to find an MD software for Windows XP operating system > Is there any? I found Gromacs which I think can be installed on both Linux and Windows system.But I dont know how to install in Windows. Could anyone please help me..or giving some ideas? Dear Ahmad, Gromacs is definitely the software worth trying. I do not have experience with Gromacs and Windows, but there is a binary version of Gromacs 3.2.1 for Windows, contributed by Peiquan Chen from China. In order to install this you just need a cpp compiler and its location set in mdp file. The package can be downloaded from: http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,48/I temid,26/ And of course, you can always compile Gromacs under Windows from the source code. By the way, personally I suggest to use Gromacs with Linux. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.comhttp://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 Tue Apr 22 09:13:01 2008 From: "Maura Mooney mmooney05-.-qub.ac.uk" To: CCL Subject: CCL: Grid Centre Autodock4 Message-Id: <-36807-080422055630-14589-omSi0bxvV1gwA9leqYnpKA^^server.ccl.net> X-Original-From: "Maura Mooney" Date: Tue, 22 Apr 2008 05:56:26 -0400 Sent to CCL by: "Maura Mooney" [mmooney05*o*qub.ac.uk] >Hi Antonio, I appreciate your feedback, but as I'm a bit of an amateur, could you specify exactly how to do this. Obviously, my grids have to be concentrated on a portion of the receptor, but when I set the grid to 0.0, 0.0, 0.0 for x, y and z coordinates, the grid box doesn't cover the receptor, instead it covers the ligand. I did this before I ran autogrid (i.e. preparing the GPF, when I was generating the grid box). I also attempted to change the ligand centre in the DPF after generating the grids, but it didn't seem to work. I would most appreciate some advice regarding this issue, especially if you can see where I am going wrong. Much appreciated, Maura "chana]|[marionegri.it" wrote: > > Sent to CCL by: chana-,-marionegri.it > Dear Maura, > > I have found the same problem. I guess is a bug, the output maps are =20 > shifted from the indicated coordinates although everything seems to be =20 > correct in the gpf file. You can check it if you show the grids after =20 > running autogrid in ADT; there you will see that the maps are shifted =20 > > from the position you indicated and therefore ligand is docked exactly =20 > where the software says, yet not in the place you intended so. > > I have solved this problem setting the coordinates of the whole system =20 > placing the centre of the binding pocket to 0.0 0.0 0.0 and it works. =20 > I also set the mass centre of the ligand to the same position, but I =20 > reckon this would not be necessary. I guess the bug must consist in =20 > symmetry operation running wild at some point, so better in that way. > > Best regards, > > Antonio > > Quoting "mmooney05**qub.ac.uk" : > > > > > Sent to CCL by: mmooney05!A!qub.ac.uk > > Hi all, > > I have a question regarding the analysis of .dlg files in =20 > > Autodock4. I have found a solution to the problem, but don=92t know =20 > > how to carry it out. I would like to know how to shift/translate the =20 > > receptor molecule according to the value of the grid centre, =20 > > specified in the .gpf file. This problem has caused my docked ligand =20 > > to sit too far away from the receptor, thus it doesn=92t appear to be =20 > > docked. > > > > I would most appreciate some advice or suggestions regarding this issue. > > > > Many Thanx, > > Maura > > > > > > > > -=3D This is automatically added to each message by the mailing script =3D= > -http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > > http://server.ccl.net/chemistry/announcements/conferences/ > From owner-chemistry@ccl.net Tue Apr 22 09:49:01 2008 From: "Lekpa Duukori duukori*gmail.com" To: CCL Subject: CCL:G: problems with a transition state Message-Id: <-36808-080422075243-18380-+Py7MxAF1EMDx/g+3f8dnQ#%#server.ccl.net> X-Original-From: "Lekpa Duukori" Content-Type: multipart/alternative; boundary="----=_Part_5977_17407278.1208861867322" Date: Tue, 22 Apr 2008 12:57:47 +0200 MIME-Version: 1.0 Sent to CCL by: "Lekpa Duukori" [duukori%gmail.com] ------=_Part_5977_17407278.1208861867322 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello Everyone I am having some problems with a transition state optimization using Gaussian 03. I am working with fairly large silicate species of about 60 atoms. I did a transition state scan at PM3 level due to size and successfully obtained the TS points ( checked by frequency calculation at PM3 level). Subsequent optimizations at HF and B3LYP levels of theory however failed to locate this transition state. B3LYP/6-31+G(d) calculations at best get a negetive frequency corresponding to hydrogen tail wag. Does any one have some ideas of where to go from here? Thanks Lekpa ------=_Part_5977_17407278.1208861867322 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello Everyone

I am having some problems with a transition state optimization using Gaussian 03.

I am working with fairly large silicate species  of about 60 atoms.  I did a transition state scan at PM3 level due to size and successfully obtained the TS points ( checked by frequency calculation at PM3 level). Subsequent optimizations at HF and 
B3LYP levels of theory however failed to locate this transition state. B3LYP/6-31+G(d) calculations at best get a negetive frequency corresponding to hydrogen tail wag.

Does any one have some ideas of where to go from here?

Thanks

Lekpa
------=_Part_5977_17407278.1208861867322-- From owner-chemistry@ccl.net Tue Apr 22 11:21:01 2008 From: "Rainer Koch rainer.koch . uni-oldenburg.de" To: CCL Subject: CCL:G: problems with a transition state Message-Id: <-36809-080422111912-21378-oeEqXTleQjruy5Zunf97dA],[server.ccl.net> X-Original-From: Rainer Koch Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 22 Apr 2008 16:49:06 +0200 MIME-Version: 1.0 Sent to CCL by: Rainer Koch [rainer.koch^uni-oldenburg.de] Dear Lepka, did you try to read in the force constants of your successful PM3 job into the subsequent optimisations (opt(readfc))? This can help a lot as you now already follow the "correct" mode. Cheers, Rainer. Lekpa Duukori duukori*gmail.com schrieb: > Hello Everyone > > I am having some problems with a transition state optimization using > Gaussian 03. > > I am working with fairly large silicate species of about 60 atoms. I > did a transition state scan at PM3 level due to size and successfully > obtained the TS points ( checked by frequency calculation at PM3 level). > Subsequent optimizations at HF and > B3LYP levels of theory however failed to locate this transition state. > B3LYP/6-31+G(d) calculations at best get a negetive frequency > corresponding to hydrogen tail wag. > > Does any one have some ideas of where to go from here? > > Thanks > > Lekpa From owner-chemistry@ccl.net Tue Apr 22 11:55:00 2008 From: "Aurelie Perrier aurelie.perrier-pineau]-[univ-paris-diderot.fr" To: CCL Subject: CCL: Looking for a plane wave code Message-Id: <-36810-080422103929-15034-qb1yJAWj7Rhgb94hGf3L3w+*+server.ccl.net> X-Original-From: "Aurelie Perrier" Date: Tue, 22 Apr 2008 10:39:25 -0400 Sent to CCL by: "Aurelie Perrier" [aurelie.perrier-pineau^univ-paris-diderot.fr] Dear CClers, I am looking for a plane wave ab initio code which is able to carry out TDDFT calculations with hybrid XC functionals. Would you have any suggestion? Thanks in advance, Aurelie ------------------------------------------------------------------- Dr. Aurelie Perrier-Pineau Laboratoire ITODYS - CNRS UMR7086 Universit PARIS 7 Denis Diderot 1, rue Guy de la Brosse 75005 Paris - France Email : aurelie.perrier-pineau(!)univ-paris-diderot.fr ------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Apr 22 12:30:01 2008 From: "Vincent Xianlong Wang xloongw:-:yahoo.com" To: CCL Subject: CCL: How to implement your own Daylight or MACCS fingerprint? Message-Id: <-36811-080422022458-28261-gaOP29srW/7rZgIXnEq9eQ-,-server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Type: text/plain; charset=us-ascii Date: Mon, 21 Apr 2008 22:24:29 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw[a]yahoo.com] Dear Jay, You may check the open source project, OpenBabel. I remember that Daylight fingerprint has been implemented in the package. Best regards, Vincent ----- Original Message ---- > From: Tiejun Cheng tjcheng.:.mail.sioc.ac.cn To: "Wang, Xianlong " Sent: Tuesday, April 22, 2008 10:36:49 AM Subject: CCL: How to implement your own Daylight or MACCS fingerprint? Sent to CCL by: "Tiejun Cheng" [tjcheng:_:mail.sioc.ac.cn] Hi all, Anyone know or any clue on how to implement the Daylight or MACCS fingerprint? These two are very useful. Sincerely, Jayhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From owner-chemistry@ccl.net Tue Apr 22 13:25:00 2008 From: "Alexander Hoepker achoepker!^!gmail.com" To: CCL Subject: CCL:G: problems with a transition state Message-Id: <-36812-080422122842-11505-NQqOexXrVhkSOhmGQn1dzw##server.ccl.net> X-Original-From: "Alexander Hoepker" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 22 Apr 2008 11:31:11 -0400 MIME-Version: 1.0 Sent to CCL by: "Alexander Hoepker" [achoepker!=!gmail.com] Dear Lekpa, Two suggestions: (1) you may want to reduce your basis set at HF level of theory, perhaps 3-= 21G. (2) the other way you may get around doing this (the one I would recommed) is to freeze the bonds that you expect to exhibit the imaginary frequency. For example: deprotonation N-H-C. constrain the two bondlengths with the keyword AddRedundant. Here's a bunch of keywords I would advise you to use: #T B3LYP/6-31G(d) Opt=3D(TS,noeigentest,AddRedundant,EstmFC) Test [coordinates] r1 r2 1.36 F (atom number 1, atom number 2, bondlength in =C5, fixed) r2 r3 1.36 F (atom number 2, atom number 3, bondlength in =C5, fixed) This fixes the distances between the three atoms and optimizes everything = else. noeigentest and especially the EstmFC keyword will reduce the computational cost. Then, you will need to rerun the TS optimization, this time without this constraint. #T B3LYP/6-31G(d) Opt=3D(TS,noeigentest,CalcFC) Freq Test Good luck Alex > I am having some problems with a transition state optimization using > Gaussian 03. > > I am working with fairly large silicate species of about 60 atoms. I di= d a > transition state scan at PM3 level due to size and successfully obtained = the > TS points ( checked by frequency calculation at PM3 level). Subsequent > optimizations at HF and > B3LYP levels of theory however failed to locate this transition state. > B3LYP/6-31+G(d) calculations at best get a negetive frequency correspondi= ng > to hydrogen tail wag. > > Does any one have some ideas of where to go from here? > > Thanks > > Lekpa > From owner-chemistry@ccl.net Tue Apr 22 14:00:01 2008 From: "Antonio Chana chana#,#marionegri.it" To: CCL Subject: CCL: Grid Centre Autodock4 Message-Id: <-36813-080422131301-11357-q+WUQD2h2q2VMdhuJYhQXA%x%server.ccl.net> X-Original-From: Antonio Chana Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Tue, 22 Apr 2008 19:11:25 +0200 MIME-version: 1.0 Sent to CCL by: Antonio Chana [chana+/-marionegri.it] Hi Maura, the point is shifting the whole protein in order to place the binding pocket centre into the origin. I mean, this is an external preparation before even preparing the grid files. Doing this, when you set the box centre to 0.0 0.0 0.0 it will cover the binding pocket perfectly. Same procedure for the ligand, that will start the docking upon the very centre of the grid box, although I still think this is not necessary at all, since autodock will place the ligand within the grid map automatically when the docking starts. I don't know the software you are using for manipulating the raw pdb file (the moment you have to set the new coordinates for the protein), but in sybyl, for instance, you can do that using the command center view (selecting a dummy atom corresponding to the center of mass already prepared) from the view menu followed by freeze view for mol area and background. Antonio Maura Mooney mmooney05-.-qub.ac.uk wrote: > Sent to CCL by: "Maura Mooney" [mmooney05*o*qub.ac.uk] > > >> Hi Antonio, >> > I appreciate your feedback, but as I'm a bit of an amateur, could you specify exactly how to do this. Obviously, my grids have to be concentrated on a portion of the receptor, but when I set the grid to 0.0, 0.0, 0.0 for x, y and z coordinates, the grid box doesn't cover the receptor, instead it covers the ligand. I did this before I ran autogrid (i.e. preparing the GPF, when I was generating the grid box). I also attempted to change the ligand centre in the DPF after generating the grids, but it didn't seem to work. > > I would most appreciate some advice regarding this issue, especially if you can see where I am going wrong. > > Much appreciated, > Maura > > "chana]|[marionegri.it" wrote: > >> Sent to CCL by: chana-,-marionegri.it >> Dear Maura, >> >> I have found the same problem. I guess is a bug, the output maps are =20 >> shifted from the indicated coordinates although everything seems to be =20 >> correct in the gpf file. You can check it if you show the grids after =20 >> running autogrid in ADT; there you will see that the maps are shifted =20 >> >>> from the position you indicated and therefore ligand is docked exactly =20 >>> >> where the software says, yet not in the place you intended so. >> >> I have solved this problem setting the coordinates of the whole system =20 >> placing the centre of the binding pocket to 0.0 0.0 0.0 and it works. =20 >> I also set the mass centre of the ligand to the same position, but I =20 >> reckon this would not be necessary. I guess the bug must consist in =20 >> symmetry operation running wild at some point, so better in that way. >> >> Best regards, >> >> Antonio >> >> Quoting "mmooney05**qub.ac.uk" : >> >> >>> Sent to CCL by: mmooney05!A!qub.ac.uk >>> Hi all, >>> I have a question regarding the analysis of .dlg files in =20 >>> Autodock4. I have found a solution to the problem, but don=92t know =20 >>> how to carry it out. I would like to know how to shift/translate the =20 >>> receptor molecule according to the value of the grid centre, =20 >>> specified in the .gpf file. This problem has caused my docked ligand =20 >>> to sit too far away from the receptor, thus it doesn=92t appear to be =20 >>> docked. >>> >>> I would most appreciate some advice or suggestions regarding this issue. >>> >>> Many Thanx, >>> Maura >>> >>> >>> >>> -=3D This is automatically added to each message by the mailing script =3D= >>> >> -http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >> >>> http://server.ccl.net/chemistry/announcements/conferences/> > > > -- Antonio Chana Ph. D. Chimica e Tossicologia dell'Ambiente Department. Istituto di Ricerche Farmacologiche "Mario Negri". Via La Masa, 19. Milano, 20156. Tel: +39 0239014394 Fax: +39 0239014735 E-mail: chana++marionegri.it From owner-chemistry@ccl.net Tue Apr 22 14:34:01 2008 From: "shentan chen modigger-.-gmail.com" To: CCL Subject: CCL:G: Gaussian 03 SCF converge problem. Message-Id: <-36814-080422114214-31294-g4o7he2DueXu++LGDBCL2w[-]server.ccl.net> X-Original-From: "shentan chen" Date: Tue, 22 Apr 2008 11:42:10 -0400 Sent to CCL by: "shentan chen" [modigger . gmail.com] Dear All, I am running DFT calculations on three organometallic ions(LnCr, LnMo and LnW, where Ln are the same ligands) using Gaussian 03. All the calculations were run under C3v symmetry. Only the job of Cr can be done normally and the jobs of Mo and W always ended with SCF converge failure. Why is that? How to solve this problem? Thanks for your help, shentan The following are parts of my input and output: Input # opt freq pw91pw91 genecp title 1 2 W N,1,B1 Output: .......... EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.625D-15 EnCoef did 100 forward-backward iterations EnCoef did 100 forward-backward iterations Restarting incremental Fock formation. ........... EnCoef did 1 forward-backward iterations Matrix for removal 9 Erem= -466.949785517310 Crem= 0.000D+00 Density matrix is not changing but DIIS error= 1.16D-02 CofLast= 1.00D-04. The SCF is confused. Error termination via Lnk1e in /usr/local/g03d01/g03/l502.exe at Mon Apr 21 17:49:22 2008. From owner-chemistry@ccl.net Tue Apr 22 15:47:01 2008 From: "shentan chen modigger###gmail.com" To: CCL Subject: CCL:G: Gaussian 03 SCF converge problem. Message-Id: <-36815-080422123556-19671-08vpNhgOvpTe2hB913LMaw]|[server.ccl.net> X-Original-From: shentan chen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 22 Apr 2008 10:53:29 -0400 MIME-Version: 1.0 Sent to CCL by: shentan chen [modigger ~~ gmail.com] Dear All, I am running DFT calculations on three organometallic ions(LnCr, LnMo and LnW, where Ln are the same ligands) using Gaussian 03. All the calculations were run under C3v symmetry. Only the job of Cr can be done normally and the jobs of Mo and W always ended with SCF converge failure. Why is that? How to solve this problem? Thanks for your help, shentan The following are parts of my input and output: Input # opt freq pw91pw91 genecp title 1 2 W N,1,B1 Output: ........... EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.625D-15 EnCoef did 100 forward-backward iterations EnCoef did 100 forward-backward iterations Restarting incremental Fock formation. ............ EnCoef did 1 forward-backward iterations Matrix for removal 9 Erem= -466.949785517310 Crem= 0.000D+00 Density matrix is not changing but DIIS error= 1.16D-02 CofLast= 1.00D-04. The SCF is confused. Error termination via Lnk1e in /usr/local/g03d01/g03/l502.exe at Mon Apr 21 17:49:22 2008. From owner-chemistry@ccl.net Tue Apr 22 16:21:01 2008 From: "David Gallagher gallagher.da!^!gmail.com" To: CCL Subject: CCL:G: [CCL:] problems with a transition state Message-Id: <-36816-080422160721-4916-D4wf5evuzSHrKN9jYUzeHQ#server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_87869265==.ALT" Date: Tue, 22 Apr 2008 12:56:33 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da]_[gmail.com] --=====================_87869265==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Lekpa, There are various ways to skin the transition state cat. Here are a few ideas that have worked for me in the past: 1. Starting from the semiempirical transition state, lock just the atoms (or bonds) of the bonds that are making and breaking in the transition state, then run a normal energy minimization to allow the rest of the molecules to relax. Finally, unlock all atoms (or bonds) and run the minimize gradient, then check that the single negative vibration is on the correct atoms. 2. If that doesn't work, try starting from an alternative semiempirical transition state such as AM1 or PM6. Personally, I seem to have had more successes from the new PM6 method. 3. If that doesn't work, you may need to manually adjust the starting point from the semiempirical transition state. First, check whether it is collapsing to reactants or products then, using the semiempirical IRC, move back a little way (off the transition state) in the opposite direction (i.e. if you are ending up with "products", then move a little way down the "reactant" side of the IRC). Save this geometry and if necessary, loop back to No. 1 (above) i.e. lock the moving atoms, etc. If the first point doesn't work, then move a little further down the IRC for the next attempt. 4. Try various combinations of the above. Finding transition states is still as much an art as it is a science! Finally, there is a overview guide to finding transition states which also mentions some other strategies at: http://www.cacheresearch.com/presentations.html Good luck, David Gallagher CACheResearch.com (Old chemists never die, they just fail to react) At 03:57 AM 4/22/2008, Lekpa Duukori duukori*gmail.com wrote: >Hello Everyone > >I am having some problems with a transition state optimization using >Gaussian 03. > >I am working with fairly large silicate species of about 60 >atoms. I did a transition state scan at PM3 level due to size and >successfully obtained the TS points ( checked by frequency >calculation at PM3 level). Subsequent optimizations at HF and >B3LYP levels of theory however failed to locate this transition >state. B3LYP/6-31+G(d) calculations at best get a negetive frequency >corresponding to hydrogen tail wag. > >Does any one have some ideas of where to go from here? > >Thanks > >Lekpa --=====================_87869265==.ALT Content-Type: text/html; charset="us-ascii" Hi Lekpa,

There are various ways to skin the transition state cat. Here are a few ideas that have worked for me in the past:

1. Starting from the semiempirical transition state, lock just the atoms (or bonds) of the bonds that are making and breaking in the transition state, then run a normal energy minimization to allow the rest of the molecules to relax. Finally, unlock all atoms (or bonds) and run the minimize gradient, then check that the single negative vibration is on the correct atoms.

2. If that doesn't work, try starting from an alternative semiempirical transition state such as AM1 or PM6. Personally, I seem to have had more successes from the new PM6 method.

3. If that doesn't work, you may need to manually adjust the starting point from the semiempirical transition state.  First, check whether it is collapsing to reactants or products then, using the semiempirical IRC, move back a little way (off the transition state) in the opposite direction (i.e. if you are ending up with "products", then move a little way down the "reactant" side of the IRC).  Save this geometry and if necessary, loop back to No. 1 (above) i.e. lock the moving atoms, etc.   If the first point doesn't work, then move a little further down the IRC for the next attempt.

4. Try various combinations of the above. Finding transition states is still as much an art as it is a science!

Finally, there is a overview guide to finding transition states which also mentions some other strategies at: http://www.cacheresearch.com/presentations.html

Good luck,
David Gallagher
CACheResearch.com

(Old chemists never die, they just fail to react)


At 03:57 AM 4/22/2008, Lekpa Duukori duukori*gmail.com wrote:
Hello Everyone

I am having some problems with a transition state optimization using Gaussian 03.

I am working with fairly large silicate species  of about 60 atoms.  I did a transition state scan at PM3 level due to size and successfully obtained the TS points ( checked by frequency calculation at PM3 level). Subsequent optimizations at HF and 
B3LYP levels of theory however failed to locate this transition state. B3LYP/6-31+G(d) calculations at best get a negetive frequency corresponding to hydrogen tail wag.

Does any one have some ideas of where to go from here?

Thanks

Lekpa
--=====================_87869265==.ALT-- From owner-chemistry@ccl.net Tue Apr 22 16:57:01 2008 From: "Konstantin Kudin konstantin_kudin_._yahoo.com" To: CCL Subject: CCL:G: Gaussian 03 SCF converge problem. Message-Id: <-36817-080422160522-4042-e6RBGAM9hA5D4m2gjiZ2kg]*[server.ccl.net> X-Original-From: Konstantin Kudin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 22 Apr 2008 13:05:03 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Konstantin Kudin [konstantin_kudin++yahoo.com] Hi Shentan, The behavior you see is due to the fact that the minimum electronic energy configuration for your specific computational method [ pw91pw91 ] is a fractionally occupied state. To fix this you should run with some level shift and DIIS (no EDIIS), then the calculation will converge, but you'll have holes (unoccupied state(s) ) below the highest occupied energy level. Alternatively, you could use a hybrid DFT method such as B3LYP, which is much less prone to get fractionally occupied states due to its use of the exact exchange. You can find out more in: E. Cancès, J. Chem. Phys. 114, 10616 (2001). E. Cancès et al., J. Chem. Phys. 118, 5364 (2003). http://dx.doi.org/10.1051/m2an:2007022 I hope this helps. Regards, Konstantin --- "shentan chen modigger-.-gmail.com" wrote: > > Sent to CCL by: "shentan chen" [modigger . gmail.com] > Dear All, > > I am running DFT calculations on three organometallic ions(LnCr, LnMo > and LnW, where Ln are the same ligands) using Gaussian 03. All the > calculations were run under C3v symmetry. Only the job of Cr can be > done normally and the jobs of Mo and W always ended with SCF > converge failure. Why is that? How to solve this problem? > Thanks for your help, > shentan > > The following are parts of my input and output: > > Input > # opt freq pw91pw91 genecp > title > 1 2 > W > N,1,B1 > > Output: > .......... > EnCoef did 100 forward-backward iterations > Rare condition: small coef for last iteration: 0.625D-15 > EnCoef did 100 forward-backward iterations > EnCoef did 100 forward-backward iterations > Restarting incremental Fock formation. > ........... > EnCoef did 1 forward-backward iterations > Matrix for removal 9 Erem= -466.949785517310 Crem= 0.000D+00 > Density matrix is not changing but DIIS error= 1.16D-02 CofLast= > 1.00D-04. > The SCF is confused. > Error termination via Lnk1e in /usr/local/g03d01/g03/l502.exe at Mon > Apr 21 17:49:22 2008. > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From owner-chemistry@ccl.net Tue Apr 22 17:32:01 2008 From: "Soren Eustis soreneustis!=!gmail.com" To: CCL Subject: CCL:G: Gaussian 03 SCF converge problem. Message-Id: <-36818-080422163337-22542-pYhTgfGoItD5b5LZiOwvhQ=server.ccl.net> X-Original-From: "Soren Eustis" Content-language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 22 Apr 2008 15:38:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soreneustis{}gmail.com] You can try a different guess option (guess=huckel, guess=indo) or you may need to use scf=qc in order to achieve convergence. -----Original Message----- > From: owner-chemistry- -ccl.net [mailto:owner-chemistry- -ccl.net] Sent: Tuesday, April 22, 2008 11:42 AM To: Eustis, Soren Subject: CCL:G: Gaussian 03 SCF converge problem. Sent to CCL by: "shentan chen" [modigger . gmail.com] Dear All, I am running DFT calculations on three organometallic ions(LnCr, LnMo and LnW, where Ln are the same ligands) using Gaussian 03. All the calculations were run under C3v symmetry. Only the job of Cr can be done normally and the jobs of Mo and W always ended with SCF converge failure. Why is that? How to solve this problem? Thanks for your help, shentan The following are parts of my input and output: Input # opt freq pw91pw91 genecp title 1 2 W N,1,B1 Output: .......... EnCoef did 100 forward-backward iterations Rare condition: small coef for last iteration: 0.625D-15 EnCoef did 100 forward-backward iterations EnCoef did 100 forward-backward iterations Restarting incremental Fock formation. ........... EnCoef did 1 forward-backward iterations Matrix for removal 9 Erem= -466.949785517310 Crem= 0.000D+00 Density matrix is not changing but DIIS error= 1.16D-02 CofLast= 1.00D-04. The SCF is confused. Error termination via Lnk1e in /usr/local/g03d01/g03/l502.exe at Mon Apr 21 17:49:22 2008.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 Tue Apr 22 21:19:01 2008 From: "Daniel - danielkimia2004!A!yahoo.com" To: CCL Subject: CCL:G: Learning Computational Message-Id: <-36819-080421105920-31059-l8xjCaY2QrhjHqTfxaEEYg{:}server.ccl.net> X-Original-From: Daniel - Content-Type: multipart/alternative; boundary="0-1332217604-1208786652=:27644" Date: Mon, 21 Apr 2008 07:04:12 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Daniel - [danielkimia2004^_^yahoo.com] --0-1332217604-1208786652=:27644 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable I suggest to you to read "Exploring Chemistry with Electronic Structure Met= hods" by =0AForesman and Frisch and "Gaussian O3 User'Reference"=0A=0ABest = regard,=0A =0ADaniel=0AChemistry ITB=0A=0A----- Original Message ----=0AFro= m: Amin Ordikhani-Seyedlar a.ordikhani/agmail.com = =0ATo: "-, Daniel - " =0ASent: Sunday, A= pril 20, 2008 18:38:02=0ASubject: CCL:G: Learning Computational=0A=0A=0ASen= t to CCL by: "Amin Ordikhani-Seyedlar" [a.ordikhani:_:gmail.com]=0AHi all,= =0Aapologize me for taking your time with my low level question. I'm a mast= er student of analytical chemistry but really keen to learn computational (= as it is so powerful). I have some beginner experiments on Gaussian03. I wa= nna predict the behaviour of molecules in different situations and ...=0AI = wanna ask you if you were me how you would start learning? There is no one = in my university that can help me so I have to learn from books and also CC= L really helps me.=0AThanks in advance.=0A=0A=0A=0A-=3D This is automatical= ly added to each message by the mailing script =3D-=0ATo recover the email = address of the author of the message, please change=0Athe strange character= s on the top line to the |,| sign. You can also=0Alook up the X-Original-From= : line in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY|,|ccl.net or= use:=0A=0A=0AE-mail t= o administrators: CHEMISTRY-REQUEST|,|ccl.net or use=0A http://www.ccl.n= et/cgi-bin/ccl/send_ccl_message=0A=0A=0A http:/= /www.ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time= at: http://www.ccl.net=0A=0A=0AConferences: h= ttp://server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messa= ges: http://www.ccl.net/htdig (login: ccl, Password: search)=0A=0AIf your = mail bounces from CCL with 5.7.1 error, check:=0A http://www.ccl.net/s= pammers.txt=0A=0A= =0A=0A=0A=0A=0A=0A=0A=0ASend instant messages to your online friends http:/= /uk.messenger.yahoo.com --0-1332217604-1208786652=:27644 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
I suggest to you to read "Exploring Chemistry with Electron= ic Structure Methods" by
Foresman and Frisch and "Gaussian O3 User'Refe= rence"

Best regard,
 
Daniel
Chemistry = ITB

----- Original Message ----
From: Amin Ordikhani-Seye= dlar a.ordikhani/agmail.com <owner-chemistry|,|ccl.net>
To: "-, Dani= el - " <danielkimia2004|,|yahoo.com>
Sent: Sunday, April 20,= 2008 18:38:02
Subject: CCL:G: Learning Computational


Sent to= CCL by: "Amin  Ordikhani-Seyedlar" [a.ordikhani:_:gmail.com]
Hi al= l,
apologize me for taking your time with my low level question. I'm a master student of analytical chemistry but really keen to learn computatio= nal (as it is so powerful). I have some beginner experiments on Gaussian03.= I wanna predict the behaviour of molecules in different situations and ...=
I wanna ask you if you were me how you would start learning? There is n= o one in my university that can help me so I have to learn from books and a= lso CCL really helps me.
Thanks in advance.



-=3D This is = automatically added to each message by the mailing script =3D-
To recove= r the email address of the author of the message, please change
the stra= nge characters on the top line to the |,| sign. You can also
look up the X= -Original-From: line in the mail header.

E-mail to subscribers: CHEMI= STRY|,|ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
<= br>E-mail to administrators: CHEMISTRY-REQUEST|,|ccl.net o= r use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_me= ssage
      http://www= ..ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait ti= me at: http://www.ccl.net<= /a>

Job: http:= //www.ccl.net/jobs
Conferences: http://server.ccl.net= /chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/htd= ig  (login: ccl, Password: search)

If your mail bounces fro= m CCL with 5.7.1 error, check:
      http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/<= /a>




Send instant messages to your onli= ne friends http://uk.messenger.yahoo.com --0-1332217604-1208786652=:27644--