From owner-chemistry@ccl.net Thu Jan 6 06:06:00 2011 From: "Herbert Fruchtl herbert.fruchtl-*-st-andrews.ac.uk" To: CCL Subject: CCL: Metalloorganic modeling Message-Id: <-43532-110106060318-7517-kK+KbebOfH6BAucR4QS4EQ(-)server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 06 Jan 2011 11:02:37 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl%a%st-andrews.ac.uk] I have no experience with Hyperchem, but... Semiempirical methods need to be parametrised for every element individually. Metals are particularly tricky, and for most of the older methods, parameters for transition metals don't exist (they may have been done separately later, but with the original AM1 and PM3, you're out of luck). As far as I know, only PM6 has been done for the whole periodic table, but I would take any semiempirical calculation involving TM metals with a large grain of salt (I just tried one, and didn't like the result). DFT should work, but choose functional (and possibly pseudopotential) carefully. HTH, Herbert Adam Mark Vogt aavogt : ymail.com wrote: > Sent to CCL by: "Adam Mark Vogt" [aavogt[A]ymail.com] > I was trying to obtain electrotopologic descriptors for a 3D-QSAR model of a set of organopalladates, and it showed that nothing of the available forcefields (at least that I know of) are not parametrized for transition metals (in my case; palladium). So, I tried to conduct semi-empirical as well as ab initio calculations to calculate point charges using hyperchem, yet regardless of the basis set or method, an error message about the atomic number being not supported always comes out. > > My questions is, is there some method to successfully simulate the electronic environment at the metal core and its surrounding? > > Thanks in Advance, > Adam Vogt.> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Thu Jan 6 06:40:01 2011 From: "Vishal Handa vishal.kohli]|[hotmail.com" To: CCL Subject: CCL: reforming a crystal dimer Message-Id: <-43533-110106061824-19129-ot6J4rFeXFC3oqHCHwQR0A-.-server.ccl.net> X-Original-From: "Vishal Handa" Date: Thu, 6 Jan 2011 06:18:23 -0500 Sent to CCL by: "Vishal Handa" [vishal.kohli**hotmail.com] Hi, was wondering if anyone could help me reform a crystal dimer from its monomer, any help would be greatly appreciated thanks Vishal From owner-chemistry@ccl.net Thu Jan 6 08:05:01 2011 From: "Jacco van de Streek vandestreek.:.avmatsim.de" To: CCL Subject: CCL: reforming a crystal dimer Message-Id: <-43534-110106080202-24273-l1+5zn3nN7gd/fIkuQHvPQ|a|server.ccl.net> X-Original-From: Jacco van de Streek Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 06 Jan 2011 14:01:26 +0100 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [vandestreek!^!avmatsim.de] On 01/06/2011 12:18 PM, Vishal Handa vishal.kohli]|[hotmail.com wrote: > was wondering if anyone could help me reform a crystal dimer from its monomer, > any help would be greatly appreciated You can probably use Mercury http://www.ccdc.cam.ac.uk/products/mercury/ to do this. Mercury is free and is available for many platforms. Mercury can read a crystal structure file (.cif. .res or .pdb), display various packings on the screen then save what is displayed on the screen to a .xyz file. The crystal structure files contain atomic coordinates of a monomer ("the asymmetric unit") as fractional coordinates, and dimers etc. are implicitly included through the space-group symmetry. A .xyz file contains the atomic coordinates as Cartesian coordinates and all atoms are explicitly in the file. Of course, this assumes that you have the actual crystal structure available, with fractional coordinates, unit cell and space-group symmetry, not just literally the Cartesian coordinates of the monomer... Best wishes, -- Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany From owner-chemistry@ccl.net Thu Jan 6 08:39:00 2011 From: "Stan van Gisbergen vangisbergen a scm.com" To: CCL Subject: CCL: ADF2010.02 released with ReaxFF and MOPAC2009 Message-Id: <-43535-110106052102-18746-CHX/7O48sygNDgN7PGo5Bg|*|server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-162-322001850 Date: Thu, 6 Jan 2011 11:21:37 +0100 Mime-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: Stan van Gisbergen [vangisbergen---scm.com] --Apple-Mail-162-322001850 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Dear CCL subscribers, Scientific Computing & Modelling (SCM) recently released version = ADF2010.02 of the Amsterdam Density Functional package. This release contains two important new modules: * The ReaxFF program, for reactive molecular dynamics simulations=20 * Dr. Stewart's MOPAC2009 binaries, which are available free of charge = to academic users.=20 Full details on all new features: http://www.scm.com/Doc/Doc2010/Background/Updates/page4.html http://www.scm.com/News/ADF2010.02.html If you wish to try ReaxFF and/or MOPAC2009 with our graphical interfaces = for them, please use the trial form (http://www.scm.com/trial). This will also allow you to test our DFT codes ADF (molecules) and BAND = (periodic structures) and our COSMO-RS program, for all of which the = recent improvements are summarized here:=20 http://www.scm.com/Doc/Doc2010/Background/Updates/page10.html=20 Many thanks are due to Prof. van Duin's group for the collaboration on = ReaxFF and to Dr. Stewart for allowing SCM to act as a value-added = reseller for MOPAC2009. =20 With all the best wishes for 2011, Stan van Gisbergen, on behalf of the SCM team. Dr. S.J.A. van Gisbergen Chief Executive Officer Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands =20 vangisbergen(!)scm.com =20 http://www.scm.com T: +31-20-5987626 =20 F: +31-20-5987629= --Apple-Mail-162-322001850 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii
Dear CCL subscribers,

Scientific Computing & = Modelling (SCM) recently released version ADF2010.02 of the Amsterdam = Density Functional package.
This release contains two important new = modules:
* The ReaxFF program, for = reactive molecular dynamics simulations 
* Dr. Stewart's MOPAC2009 binaries, which are = available free of charge to academic = users. 
Full details on all new = features:
If = you wish to try ReaxFF and/or MOPAC2009 with our graphical interfaces = for them, please use the trial form (http://www.scm.com/trial).
This will also allow you = to test our DFT codes ADF (molecules) and BAND (periodic structures) and = our COSMO-RS program, for all of which the recent improvements are = summarized here: 

Many thanks are due to = Prof. van Duin's group for the collaboration on ReaxFF and to Dr. = Stewart for allowing SCM to act as a value-added reseller for MOPAC2009. =  

With all the best wishes for = 2011,
Stan van Gisbergen, on = behalf of the SCM team.
Dr. S.J.A. van Gisbergen
Chief Executive Officer
De = Boelelaan 1083
1081 HV Amsterdam
The Netherlands         =                     =    
T: +31-20-5987626    
F: = +31-20-5987629
= = --Apple-Mail-162-322001850-- From owner-chemistry@ccl.net Thu Jan 6 09:14:00 2011 From: "Soren Eustis soreneustis]^[gmail.com" To: CCL Subject: CCL:G: help Message-Id: <-43536-110106054635-25143-gMbwaR/kkwxAvQSw39PSgw++server.ccl.net> X-Original-From: Soren Eustis Content-type: multipart/alternative; boundary="B_3377159158_4108613" Date: Thu, 06 Jan 2011 11:45:55 +0100 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis#,#gmail.com] > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3377159158_4108613 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Greetings. The issue here is that the number of optimization steps is exceeded. Gaussian has a built in maximum that is predetermined from the size (number if redundant internal coordinates) of the system under study. Therefore, if you ask for maxcycles=3D999 and the built in limit for a two water system works out to be 100 =AD the run will stop after 100 cycles. Thi= s is not all that unusual with a vdW system like a water dimer. You can look at the energies and forces for each step and see whether they are steadily approaching their limits or if they are oscillating around a shallow potential well. In either case, I would take the final (step 100) geometry and start a new calculation from there. Use the opt(maxcycles=3D100, maxstep=3D10) keywords. The latter is what will allow convergence as Gaussia= n is likely making optimization steps that are too large for such a shallow well. Secondly, I would always use some extra diffuse functions for a non-covalently bonded complex. If this does not work, there are a few other tricks you can play with to find the minima. Gaussian's online manual has more information (http://www.gaussian.com/g_tech/g_ur/k_opt.htm) Regards, Soren -- Soren N. Eustis, Ph.D. ETH =AD Zurich Environmental Organic Chemistry Group Institute for Biogeochemistry and Pollutant Dynamics Universitatstrasse 16 CHN F33 8092 Zurich +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren__env.ethz.ch > From: "Delwar Hossain hossaind2004+*+yahoo.com" Reply-To: Ccl Date: Wed, 5 Jan 2011 08:25:16 -0800 (PST) To: Soren Eustis Subject: CCL:G: help Increase number of optimization step. If water molecule is oscillating back and forth in a very shallow potential energy surface, using CalcFC (or SCF=3DQC) may help. Thanks, Delwar > From: "Bilel Mansouri bilelmansouri80-,-yahoo.fr" To: "Hossain, Delwar " Sent: Tue, January 4, 2011 11:51:53 AM Subject: CCL:G: help >=20 >=20 >>=20 >>>=20 >>>>=20 >>>>=20 >>>> HI >>>>> > I'm doing a (what I thought was simple) test job of tow water molec= ules >>>>> whith supermolecule methode using B3LYP >>>> and I use the following input job >>>> # opt=3D(modredundant,maxcycles=3D999), Int(Grid=3DULTRAFIN) B3LYP/6-311g >>>> g counterpoise=3D2 >>>> I have the error message and i use the keyword int=3Dgrid=3Dultrafine >>>> =20 >>>> =20 >>>> Item Value Threshold Converged? >>>> Maximum Force 0.000882 0.000450 NO >>>> RMS Force 0.000269 0.000300 NO >>>>> Maximum Displacement 0.056470 0.001800 NO >>>>> RMS Displacement 0.014132 0.001200 NO >>>>> Predicted change in Energy=3D-1.659919D-03 >>>>> Optimization stopped. >>>>> -- Number of steps exceeded, NStep=3D 100 >>>>> -- Flag reset to prevent archiving. >>>>> ---------------------------- >>>>> ! Non-Optimized Parameters ! >>>>> ! (Angstroms and Degrees) ! >>>>> -------------------------- >>>>> -------------------------- >>>>> ! Name Definition Value Derivative Info. >>>>> ! >>>>> =20 >>>>> ---------------------------------------------------------------------= ----- >>>>> ------ >>>>> ! R1 R(1,3) 3.9996 -DE/DX =3D -0.0023 >>>>> ! >>>>> ! R2 R(1,5) 1.003 -DE/DX =3D 0.0 >>>>> ! >>>>> ! R3 R(1,6) 1.003 -DE/DX =3D 0.0 >>>>> ! >>>>> ! R4 R(1,7) 2.9817 -DE/DX =3D -0.0009 >>>>> ! >>>>> ! R5 R(1,9) 3.0732 -DE/DX =3D -0.001 >>>>> ! >>>>> ! R6 R(2,4) 3.9997 -DE/DX =3D -0.0029 >>>>> ! >>>>> ! R7 R(2,7) 0.9737 -DE/DX =3D 0.0004 >>>>> ! >>>>> ! R8 R(2,8) 0.9697 -DE/DX =3D 0.0007 >>>>> ! >>>>> ! R9 R(3,9) 0.9722 -DE/DX =3D -0.0013 >>>>> ! >>>>> ! R10 R(3,10) 0.9664 -DE/DX =3D -0.0001 >>>>> ! >>>>> ! R11 R(3,11) 1.7428 -DE/DX =3D 0.0002 >>>>> ! >>>>> ! R12 R(4,8) 4.4728 -DE/DX =3D -0.0008 >>>>> ! >>>>> ! R13 R(4,11) 0.981 -DE/DX =3D 0.0003 >>>>> ! >>>>> ! R14 R(4,12) 0.9659 -DE/DX =3D 0.0 >>>>> ! >>>>> ! A1 A(3,1,5) 99.0096 -DE/DX =3D 0.0 >>>>> ! >>>>> ! A2 A(3,1,6) 99.0096 -DE/DX =3D 0.0 >>>>> ! >>>>> ! A3 A(3,1,7) 68.5648 -DE/DX =3D 0.0 >>>>> ! >>>>> ! A4 A(5,1,6) 104.9845 -DE/DX =3D -0.0007 >>>>> ! >>>>> ! A5 A(5,1,7) 60.6293 -DE/DX =3D -0.0003 >>>>> ! >>>>> ! A6 A(5,1,9) 101.859 -DE/DX =3D 0.0001 >>>>> ! >>>>> ! A7 A(6,1,7) 60.6293 -DE/DX =3D -0.0003 >>>>> ! >>>>> ! A8 A(6,1,9) 101.859 -DE/DX =3D 0.0001 >>>>> ! >>>>> ! A9 A(7,1,9) 73.3866 -DE/DX =3D 0.0 >>>>> ! >>>>> ! A10 A(4,2,7) 3.2523 -DE/DX =3D 0.001 >>>>> ! >>>>> ! A11 A(7,2,8) 110.0485 -DE/DX =3D 0.0001 >>>>> ! >>>>> ! A12 A(1,3,10) 126.5996 -DE/DX =3D 0.0001 >>>>> ! >>>>> ! A13 A(1,3,11) 96.7028 -DE/DX =3D -0.0001 >>>>> ! >>>>> ! A14 A(9,3,10) 111.1913 -DE/DX =3D -0.0001 >>>>> ! >>>>> ! A15 A(9,3,11) 112.1111 -DE/DX =3D 0.0001 >>>>> ! >>>>> ! A16 A(10,3,11) 136.6976 -DE/DX =3D 0.0 >>>>> ! >>>>> ! A17 A(2,4,11) 95.2594 -DE/DX =3D -0.0002 >>>>> ! >>>>> ! A18 A(2,4,12) 154.9369 -DE/DX =3D -0.0001 >>>>> ! >>>>> ! A19 A(8,4,11) 106.7444 -DE/DX =3D -0.0002 >>>>> ! >>>>> ! A20 A(8,4,12) 143.4519 -DE/DX =3D -0.0001 >>>>> ! >>>>> ! A21 A(11,4,12) 109.8037 -DE/DX =3D 0.0003 >>>>> ! >>>>> ! A22 L(1,7,2,4,-1) 285.8641 -DE/DX =3D -0.0011 >>>>> ! >>>>> ! A23 L(3,11,4,2,-1) 168.2659 -DE/DX =3D -0.0003 >>>>> ! >>>>> ! A24 L(1,7,2,4,-2) 180.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! A25 L(3,11,4,2,-2) 180.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D1 D(3,1,2,4) 0.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D2 D(3,1,2,8) 180.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D3 D(5,1,2,4) 102.9058 -DE/DX =3D 0.0001 >>>>> ! >>>>> ! D4 D(5,1,2,8) -77.0942 -DE/DX =3D 0.0001 >>>>> ! >>>>> ! D5 D(6,1,2,4) -102.9058 -DE/DX =3D -0.0001 >>>>> ! >>>>> ! D6 D(6,1,2,8) 77.0942 -DE/DX =3D -0.0001 >>>>> ! >>>>> ! D7 D(9,1,2,4) 0.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D8 D(9,1,2,8) 180.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D9 D(5,1,3,10) 126.5651 -DE/DX =3D 0.0004 >>>>> ! >>>>> ! D10 D(5,1,3,11) -53.4349 -DE/DX =3D 0.0004 >>>>> ! >>>>> ! D11 D(6,1,3,10) -126.5651 -DE/DX =3D -0.0004 >>>>> ! >>>>> ! D12 D(6,1,3,11) 53.4349 -DE/DX =3D -0.0004 >>>>> ! >>>>> ! D13 D(7,1,3,10) 180.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D14 D(7,1,3,11) 0.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D15 D(7,2,4,11) 180.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D16 D(7,2,4,12) 0.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D17 D(1,3,4,2) 0.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D18 D(1,3,4,8) 0.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D19 D(1,3,4,12) 180.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D20 D(9,3,4,2) 0.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D21 D(9,3,4,8) 0.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D22 D(9,3,4,12) 180.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D23 D(10,3,4,2) 180.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D24 D(10,3,4,8) 180.0 -DE/DX =3D 0.0 >>>>> ! >>>>> ! D25 D(10,3,4,12) 0.0 -DE/DX =3D 0.0 >>>>> ! >>>>> =20 >>>>> ---------------------------------------------------------------------= ----- >>>>> ------ >>>>> GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad= Grad >>>>> Input orientation: >>>>> --------------------------------------------------------------------= - >>>>> Center Atomic Atomic Coordinates (Angstroms) >>>>> Number Number Type X Y Z >>>>> --------------------------------------------------------------------= - >>>>> 1 8 0 0.184505 0.000000 0.15498= 4 >>>>> 2 8 0 0.033034 0.000000 2.88164= 0 >>>>> 3 8 0 4.161469 0.000000 0.58365= 2 >>>>> 4 8 0 4.011921 0.000000 3.29207= 1 >>>>> 5 1 0 -0.032703 -0.765799 0.71295= 5 >>>>> 6 1 0 -0.032703 0.765799 0.71295= 5 >>>>> 7 1 0 0.995253 0.000000 3.03553= 1 >>>>> 8 1 0 -0.438867 0.000000 3.72732= 6 >>>>> 9 1 0 3.261177 0.000000 0.21567= 7 >>>>> 10 1 0 4.826475 0.000000 -0.11789= 2 >>>>> 11 1 0 4.189967 0.000000 2.32427= 6 >>>>> 12 1 0 4.842678 0.000000 3.78796= 5 >>>>> --------------------------------------------------------------------= - >>>>> Distance matrix (angstroms): >>>>> 1 2 3 4 5 >>>>> 1 O 0.000000 >>>>> 2 O 2.730860 0.000000 >>>>> 3 O 4.000000 4.724906 0.000000 >>>>> 4 O 4.948780 4.000000 2.712545 0.000000 >>>>> 5 H 0.972090 2.300862 4.265472 4.857702 0.000000 >>>>> 6 H 0.972090 2.300862 4.265472 4.857702 1.531598 >>>>> 7 H 2.992467 0.974448 4.004577 3.027557 2.652829 >>>>> 8 H 3.626323 0.968439 5.571875 4.472020 3.136535 >>>>> 9 H 3.077270 4.186678 0.972590 3.166673 3.418096 >>>>> 10 H 4.649983 5.654580 0.966641 3.505901 4.988824 >>>>> 11 H 4.555168 4.194133 1.740858 0.984036 4.584076 >>>>> 12 H 5.907378 4.894293 3.275922 0.967506 5.814764 >>>>> 6 7 8 9 10 >>>>> 6 H 0.000000 >>>>> 7 H 2.652829 0.000000 >>>>> 8 H 3.136535 1.592257 0.000000 >>>>> 9 H 3.418096 3.617456 5.101177 0.000000 >>>>> 10 H 4.988824 4.962090 6.519933 1.600445 0.000000 >>>>> 11 H 4.584076 3.272932 4.836802 2.304093 2.523753 >>>>> 12 H 5.814764 3.920311 5.281894 3.906711 3.905890 >>>>> 11 12 >>>>> 11 H 0.000000 >>>>> 12 H 1.602627 0.000000 >>>>> Stoichiometry H8O4 >>>>> Framework group CS[SG(H6O4),X(H2)] >>>>> Deg. of freedom 20 >>>>> Full point group CS >>>>> Largest Abelian subgroup CS NOp 2 >>>>> Largest concise Abelian subgroup CS NOp 2 >>>>> Standard orientation: >>>>> --------------------------------------------------------------------= - >>>>> Center Atomic Atomic Coordinates (Angstroms) >>>>> Number Number Type X Y Z >>>>> --------------------------------------------------------------------= - >>>>> 1 8 0 -2.501070 0.069787 0.00000= 0 >>>>> 2 8 0 -0.827351 2.227623 0.00000= 0 >>>>> 3 8 0 0.782472 -2.214584 0.00000= 0 >>>>> 4 8 0 2.445684 -0.071777 0.00000= 0 >>>>> 5 1 0 -2.299150 0.633470 0.76579= 9 >>>>> 6 1 0 -2.299150 0.633470 -0.76579= 9 >>>>> 7 1 0 0.000000 1.712804 0.00000= 0 >>>>> 8 1 0 -0.629035 3.175540 0.00000= 0 >>>>> 9 1 0 -0.138519 -1.901999 0.00000= 0 >>>>> 10 1 0 0.824466 -3.180313 0.00000= 0 >>>>> 11 1 0 1.945446 -0.919177 0.00000= 0 >>>>> 12 1 0 3.398064 -0.242189 0.00000= 0 >>>>> --------------------------------------------------------------------= - >>>>> Rotational constants (GHZ): 3.6566956 1.7161673 1.174= 4164 >>>>> ********************************************************************= ** >>>>> Population analysis using the SCF density. >>>>> ********************************************************************= ** >>>>> Electronic spatial extent (au): =3D 919.2008 >>>>> Charge=3D 0.0000 electrons >>>>> Dipole moment (field-independent basis, Debye): >>>>> X=3D 1.8028 Y=3D -0.6387 Z=3D 0.0000 Tot=3D 1.9126 >>>>> Quadrupole moment (field-independent basis, Debye-Ang): >>>>> XX=3D -30.6350 YY=3D -7.6894 ZZ=3D -26.4884 >>>>> XY=3D -5.0915 XZ=3D 0.0000 YZ=3D 0.0000 >>>>> Traceless Quadrupole moment (field-independent basis, Debye-Ang): >>>>> XX=3D -9.0307 YY=3D 13.9149 ZZ=3D -4.8841 >>>>> XY=3D -5.0915 XZ=3D 0.0000 YZ=3D 0.0000 >>>>> Octapole moment (field-independent basis, Debye-Ang**2): >>>>> XXX=3D 53.7799 YYY=3D -7.6173 ZZZ=3D 0.0000 XYY=3D 5.7536 >>>>> XXY=3D -2.5321 XXZ=3D 0.0000 XZZ=3D -7.1177 YZZ=3D 1.2264 >>>>> YYZ=3D 0.0000 XYZ=3D 0.0000 >>>>> Hexadecapole moment (field-independent basis, Debye-Ang**3): >>>>> XXXX=3D -509.3830 YYYY=3D -156.7525 ZZZZ=3D -23.2511 XXXY=3D 30.6051 >>>>> XXXZ=3D 0.0000 YYYX=3D 48.4794 YYYZ=3D 0.0000 ZZZX=3D 0.0000 >>>>> ZZZY=3D 0.0000 XXYY=3D -160.2397 XXZZ=3D -90.8949 YYZZ=3D -82.4570 >>>>> XXYZ=3D 0.0000 YYXZ=3D 0.0000 ZZXY=3D 26.3538 >>>>> Atom 7 needs variable 8=3D 0.9744477035 but is 0.9720898606 >>>>> Input z-matrix variables are not compatible with final structure. >>>>>=20 >>>>> FAULTILY FAULTLESS, ICILY REGULAR, SPLENDIDLY NULL... >>>>> MAUDE BY TENNYSON >>>>> Error termination request processed by link 9999. >>>>> Error termination via Lnk1e in C:\G03W\l9999.exe at Thu Nov 04 19:09= :35 >>>>> 2010. >>>>> Job cpu time: 0 days 1 hours 13 minutes 15.0 seconds. >>>>> File lengths (MBytes): RWF=3D 20 Int=3D 0 D2E=3D 0 Chk=3D = 11 >>>>> Scr=3D 1 >>>>> Any insight would be very helpful. >>>>>=20 >>>>> Thanks! >>>>>=20 >>>>=20 >>>=20 >>>=20 >>=20 >=20 =20 --B_3377159158_4108613 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable

Greetings.   The= issue here is that the number of optimization steps is exceeded.  Gaus= sian has a built in maximum that is predetermined from the size (number if r= edundant internal coordinates) of the system under study.  Therefore, i= f you ask for maxcycles=3D999 and the built in limit for a two water system wo= rks out to be 100 – the run will stop after 100 cycles.  This is = not all that unusual with a vdW system like a water dimer.  You can loo= k at the energies and forces for each step and see whether they are steadily= approaching their limits or if they are oscillating around a shallow potent= ial well.  In either case, I would take the final (step 100) geometry a= nd start a new calculation from there.  Use the opt(maxcycles=3D100, maxs= tep=3D10) keywords.  The latter is what will allow convergence as Gaussia= n is likely making optimization steps that are too large for such a shallow = well.  Secondly, I would always use some extra diffuse functions for a = non-covalently bonded complex.


If this does not work, there are a few= other tricks you can play with to find the minima.  Gaussian's online = manual has more information (http://www.gaussian.com/g_tech/g_ur/k_opt.htm)


Regards,<= /p>


Soren


--
Soren= N. Eustis, Ph.D.
<= span style=3D"font-size:11pt"> ETH – Zurich
Environmental Organic Chemistry Group
Institute for Biogeochemistry and Pollutant Dynamics
Universitatstrasse 16
CHN F33
8092 Zurich

+41 44 632 93 48 (office)
+41 44 632 14 38 (fax)

soren__env.ethz.ch=






From: "= Delwar Hossain hossaind2004+*+yahoo.com" <owner-chemistry__ccl.net>
= Reply-To: Ccl <chemistry__ccl.n= et>
Date: Wed, 5 Jan 2011 0= 8:25:16 -0800 (PST)
To: Soren Eust= is <soreneustis__gmail.com><= br>Subject: CCL:G: help

Increase number of optimization step. If water molecule is o= scillating back and forth in a very shallow potential energy surface, using = CalcFC (or SCF=3DQC) may help.
Thanks,
Delwar

From: "Bilel Mansouri bilelmansouri80-,= -yahoo.fr" <owner-chemistry[A]ccl.net>
To: "Hossain, Delwar " <hossaind2004[A]yahoo.com>Sent: Tue, January 4, 2011 11= :51:53 AM
Subject: CCL:G: h= elp

<= tr>



=




HI> I'm doing a (what I thought was simple) test job of tow wate= r molecules whith supermolecule methode using B3LYP
and I use= the following input job
= # opt=3D(modredundant,maxcycles=3D999), Int(Grid=3DULTRAFIN)  B3LYP/6-311g
g counterpoise=3D2
I have the error message  and i use the keyword int=3Dgrid=3Dult= rafine
 
 
    &= nbsp; Item           =     Value     Threshold  Converged?<= br> Maximum Force         =    0.000882     0.000450   &nbs= p; NO
 RMS     Force    &nb= sp;       0.000269     0.0= 00300     NO
Maximum Displa= cement     0.056470     0.001800&nbs= p;    NO
 RMS     Displacement&n= bsp;    0.014132     0.001200  =    NO
 Predicted change in Energy=3D-1.659919D-03
 = Optimization stopped.
    -- Number of steps exceeded,&nbs= p; NStep=3D 100
    -- Flag reset to prevent archiving.
&= nbsp;            = ;            &nb= sp; ----------------------------
      &nbs= p;            &n= bsp;       ! Non-Optimized Parameters !
           &nb= sp;            &= nbsp;  ! (Angstroms and Degrees)  !
 ---------------------= -----            = ;            &nb= sp;   --------------------------
 ! Name  Definition&= nbsp;            = ; Value          Derivative Inf= o.            &n= bsp;   !
 ------------------------------------------------= --------------------------------
 ! R1    R(1,3) = ;            &nb= sp;    3.9996         -DE/DX =3D  = ; -0.0023           &= nbsp;  !
 ! R2    R(1,5)    =             &nbs= p; 1.003          -DE/DX =3D = ;   0.0          = ;       !
 ! R3    R(1,= 6)            &n= bsp;     1.003       =    -DE/DX =3D    0.0     &nb= sp;           !
 != R4    R(1,7)        =           2.9817         -DE/DX =3D  = ; -0.0009           &= nbsp;  !
 ! R5    R(1,9)    =             &nbs= p; 3.0732         -DE/DX =3D &nbs= p; -0.001           &= nbsp;   !
 ! R6    R(2,4)   =             &nbs= p;  3.9997         -DE/DX =3D&nbs= p;  -0.0029          =     !
 ! R7    R(2,7)   = ;            &nb= sp;  0.9737         -DE/DX =3D  = ;  0.0004          &n= bsp;   !
 ! R8    R(2,8)   &= nbsp;            = ;  0.9697         -DE/DX =3D = ;   0.0007         &n= bsp;    !
 ! R9    R(3,9)  &= nbsp;            = ;   0.9722         -DE/DX = =3D   -0.0013         &= nbsp;    !
 ! R10   R(3,10)  &nbs= p;            &n= bsp; 0.9664         -DE/DX =3D  = ; -0.0001           &= nbsp;  !
 ! R11   R(3,11)    &nbs= p;            1.7428&= nbsp;        -DE/DX =3D    0= .0002            = ;  !
 ! R12   R(4,8)     &nb= sp;            4.4728=          -DE/DX =3D   -0.000= 8            &nb= sp; !
 ! R13   R(4,11)      =            0.981 &nbs= p;        -DE/DX =3D    0.0003        =       !
 ! R14   R(4,12) &nb= sp;            &= nbsp;  0.9659         -DE/DX =3D&= nbsp;   0.0         &= nbsp;       !
 ! A1    = A(3,1,5)           &n= bsp;   99.0096         -DE= /DX =3D    0.0        &= nbsp;        !
 ! A2  &= nbsp; A(3,1,6)          &n= bsp;    99.0096       &nbs= p; -DE/DX =3D    0.0            = ;     !
 ! A3    A(3,1,7) &n= bsp;            = 68.5648         -DE/DX =3D  = ;  0.0           = ;      !
 ! A4    A(5,1,6)&n= bsp;            = 104.9845         -DE/DX =3D &nbs= p; -0.0007           =    !
 ! A5    A(5,1,7)   &nb= sp;           60.6293 = ;        -DE/DX =3D   -0.0003           &= nbsp;  !
 ! A6    A(5,1,9)   &nbs= p;          101.859  =         -DE/DX =3D    0.0001=             &nbs= p; !
 ! A7    A(6,1,7)     &= nbsp;         60.6293  &nb= sp;      -DE/DX =3D   -0.0003  &n= bsp;           !
 = ! A8    A(6,1,9)       &nb= sp;      101.859      = ;    -DE/DX =3D    0.0001    = ;          !
 ! A9    A(7,1,9)     &n= bsp;         73.3866  &nbs= p;      -DE/DX =3D    0.0  &= nbsp;            = ;  !
 ! A10   A(4,2,7)     &= nbsp;          3.2523 &nbs= p;       -DE/DX =3D    0.001 = ;            &nb= sp; !
 ! A11   A(7,2,8)      = ;        110.0485    =      -DE/DX =3D    0.0001   =            !
 ! A1= 2   A(1,3,10)           = ;  126.5996         -DE/DX =3D&nb= sp;   0.0001         =      !
 ! A13   A(1,3,11)  &= nbsp;           96.7028&nb= sp;        -DE/DX =3D   -0.0001&n= bsp;            = !
 ! A14   A(9,3,10)      &= nbsp;      111.1913     &n= bsp;   -DE/DX =3D   -0.0001     &= nbsp;        !
 ! A15  = A(9,3,11)           =   112.1111         -DE/DX =3D &nb= sp;  0.0001          =     !
 ! A16   A(10,3,11)   =          136.6976   &= nbsp;     -DE/DX =3D    0.0  &nbs= p;            &n= bsp; !
 ! A17   A(2,4,11)     &nb= sp;        95.2594    = ;     -DE/DX =3D   -0.0002   &nbs= p;          !
 ! A18&nb= sp;  A(2,4,12)         &nb= sp;   154.9369         -DE= /DX =3D   -0.0001           &= nbsp;  !
 ! A19   A(8,4,11)    &n= bsp;        106.7444   &nb= sp;     -DE/DX =3D   -0.0002   &n= bsp;          !
 ! A20&= nbsp;  A(8,4,12)         &= nbsp;   143.4519         -= DE/DX =3D   -0.0001        &= nbsp;     !
 ! A21   A(11,4,12) &= nbsp;          109.8037 &n= bsp;       -DE/DX =3D    0.0003&n= bsp;            = !
 ! A22   L(1,7,2,4,-1)         285.8641&nbs= p;        -DE/DX =3D   -0.0011&nb= sp;             = !
 ! A23   L(3,11,4,2,-1)     &nb= sp;  168.2659         -DE/DX =3D&= nbsp;  -0.0003         &nb= sp;    !
 ! A24   L(1,7,2,4,-2)  =        180.0     &nbs= p;      -DE/DX =3D    0.0  &= nbsp;            = ;  !
 ! A25   L(3,11,4,2,-2)    &= nbsp;   180.0         = ;   -DE/DX =3D    0.0            = ;     !
 ! D1    D(3,1,2,4) =              0.0=             -DE/DX =3D&= nbsp;   0.0         &= nbsp;       !
 ! D2    = D(3,1,2,8)           = 180.0            -DE= /DX =3D    0.0        &= nbsp;        !
 ! D3  &= nbsp; D(5,1,2,4)          =   102.9058         -DE/DX =3D&nbs= p;   0.0001           &n= bsp;  !
 ! D4    D(5,1,2,8)   &nb= sp;        -77.0942   &nbs= p;     -DE/DX =3D    0.0001  &nbs= p;           !
 ! = D5    D(6,1,2,4)       &nb= sp;   -102.9058         -D= E/DX =3D   -0.0001        &n= bsp;     !
 ! D6    D(6,1,2,8)&nb= sp;            77.094= 2         -DE/DX =3D   -0.00= 01            &n= bsp; !
 ! D7    D(9,1,2,4)          &nbs= p;   0.0         &nbs= p;  -DE/DX =3D    0.0      &= nbsp;          !
 ! D8&= nbsp;   D(9,1,2,8)        =     180.0        &nbs= p;   -DE/DX =3D    0.0     &= nbsp;           !
 = ;! D9    D(5,1,3,10)       = ;    126.5651        = -DE/DX =3D    0.0004       =        !
 ! D10   D(5,1,3,11)           -5= 3.4349         -DE/DX =3D  &= nbsp; 0.0004          &nbs= p;   !
 ! D11   D(6,1,3,10)   &nb= sp;      -126.5651     &nb= sp;   -DE/DX =3D   -0.0004     &n= bsp;        !
 ! D12   = D(6,1,3,11)           = ; 53.4349         -DE/DX =3D &nbs= p; -0.0004           =    !
 ! D13   D(7,1,3,10)    = ;       180.0     &nb= sp;      -DE/DX =3D    0.0        &nb= sp;        !
 ! D14   D= (7,1,3,11)           =   0.0           = -DE/DX =3D    0.0       &nb= sp;         !
 ! D15 &n= bsp; D(7,2,4,11)          = 180.0            -DE= /DX =3D    0.0        &= nbsp;        !
 ! D16  = D(7,2,4,12)          &nbs= p;  0.0          &nbs= p; -DE/DX =3D    0.0            = ;     !
 ! D17   D(1,3,4,2)  = ;            0.0 = ;           -DE/DX =3D =    0.0          =        !
 ! D18   D(1,3,4,8)=             &nbs= p; 0.0            -DE= /DX =3D    0.0        &= nbsp;        !
 ! D19  = D(1,3,4,12)           180= .0            -DE/DX = =3D    0.0            = ;     !
 ! D20   D(9,3,4,2)  = ;            0.0 = ;           -DE/DX =3D =    0.0          =        !
 ! D21   D(9,3,4,8)=             &nbs= p; 0.0            -DE= /DX =3D    0.0        &= nbsp;        !
 ! D22  = D(9,3,4,12)           180= .0            -DE/DX = =3D    0.0            = ;     !
 ! D23   D(10,3,4,2) &nbs= p;         180.0   &n= bsp;        -DE/DX =3D    0.= 0            &nb= sp;    !
 ! D24   D(10,3,4,8)  &n= bsp;        180.0    =         -DE/DX =3D    0.0&nb= sp;            &= nbsp;   !
 ! D25   D(10,3,4,12)   = ;         0.0    = ;        -DE/DX =3D    0.0            = ;     !
 ---------------------------------------= -----------------------------------------
 GradGradGradGradGradGradG= radGradGradGradGradGradGradGradGradGradGradGrad
   =             &nbs= p;          Input orientation:&= nbsp;            = ;              --------------------------------------------------------------------= -
 Center     Atomic     Ato= mic            &= nbsp; Coordinates (Angstroms)
 Number     Number=       Type       = ;       X      &= nbsp;    Y        &nb= sp;  Z
 ---------------------------------------------------------------= ------
    1       &nbs= p;  8           =   0        0.184505   = ; 0.000000    0.154984
    2  &nb= sp;       8      = ;       0      &= nbsp; 0.033034    0.000000    2.881640
&nbs= p;   3          8&nbs= p;            0 =        4.161469    0.000000&nbs= p;   0.583652
    4     = ;     8             = 0        4.011921    0.000= 000    3.292071
    5   &nbs= p;      1       =       0       -0.0327= 03   -0.765799    0.712955
    6&= nbsp;         1   &nb= sp;         0    = ;   -0.032703    0.765799    0.71295= 5
    7        &nb= sp; 1            = ; 0        0.995253    0.0= 00000    3.035531
    8          1   = ;          0   &= nbsp;   -0.438867    0.000000    3.7= 27326
    9        = ;  1           &= nbsp; 0        3.261177   = 0.000000    0.215677
   10   &nb= sp;      1       = ;      0        = 4.826475    0.000000   -0.117892
   11=           1   &n= bsp;         0   &nbs= p;    4.189967    0.000000    2.324276
   12   &n= bsp;      1      &nbs= p;      0       = 4.842678    0.000000    3.787965
 ---= ------------------------------------------------------------------
 =             &nbs= p;      Distance matrix (angstroms):
  = ;            &nb= sp;     1        = ;  2          3  = ;        4     &= nbsp;    5
     1  O  &= nbsp; 0.000000
     2  O    2.730860   0.000000
   &nb= sp; 3  O    4.000000   4.724906   0.= 000000
     4  O    4.948780 = ;  4.000000   2.712545   0.000000
  &n= bsp;  5  H    0.972090   2.300862 &n= bsp; 4.265472   4.857702   0.000000
   = ;  6  H    0.972090   2.300862  = ; 4.265472   4.857702   1.531598
   &n= bsp; 7  H    2.992467   0.974448   4= .004577   3.027557   2.652829
    = ; 8  H    3.626323   0.968439   5.57= 1875   4.472020   3.136535
     9=   H    3.077270   4.186678   0.972590   3.166673   3.418096    10  H    4.649983   5.6545= 80   0.966641   3.505901   4.988824
 &= nbsp;  11  H    4.555168   4.194133 =   1.740858   0.984036   4.584076
  &nb= sp; 12  H    5.907378   4.894293   3= .275922   0.967506   5.814764
    = ;            &nb= sp;   6          7&nb= sp;         8    = ;      9       &= nbsp; 10
     6  H    0.000000     7  H    2.652829   0.000000
     8  H &= nbsp;  3.136535   1.592257   0.000000
 &nbs= p;   9  H    3.418096   3.617456&nbs= p;  5.101177   0.000000
    10  H = ;   4.988824   4.962090   6.519933  = 1.600445   0.000000
    11  H  &= nbsp; 4.584076   3.272932   4.836802   2.30409= 3   2.523753
    12  H    5.= 814764   3.920311   5.281894   3.906711 &= nbsp; 3.905890
         &nbs= p;         11    = ;     12
    11  H  &nb= sp; 0.000000
    12  H    1.602627   0.000000
 Stoichiometry&n= bsp;   H8O4
 Framework group  CS[SG(H6O4),X(H2)]
&= nbsp;Deg. of freedom    20
 Full point group &nb= sp;            &= nbsp;  CS
 Largest Abelian subgroup    &nbs= p;    CS      NOp   2
&= nbsp;Largest concise Abelian subgroup CS      NOp&n= bsp;  2
          =             &nbs= p;  Standard orientation:       &nbs= p;            &n= bsp;   
 ----------------------------------------------------------------= -----
 Center     Atomic    = Atomic           &nb= sp;  Coordinates (Angstroms)
 Number     Nu= mber      Type      &= nbsp;       X     &nb= sp;     Y        = ;   Z
 ---------------------------------------------------= ------------------
    1     &nbs= p;    8         =     0       -2.501070 &nbs= p;  0.069787    0.000000
    2 &n= bsp;        8             = 0       -0.827351    2.227623&n= bsp;   0.000000
    3    &nb= sp;     8        = ;     0        0.7824= 72   -2.214584    0.000000
    4&= nbsp;         8   &nb= sp;         0    = ;    2.445684   -0.071777    0.00000= 0
    5        &nb= sp; 1            = ; 0       -2.299150    0.633470=     0.765799
    6          1   = ;          0   &= nbsp;   -2.299150    0.633470   -0.765799=
    7        &nbs= p; 1            = 0        0.000000    1.71= 2804    0.000000
    8   &nb= sp;      1       = ;      0       -0.629= 035    3.175540    0.000000
  &nb= sp; 9          1  &nb= sp;          0   = ;    -0.138519   -1.901999    0.000000
   10   &= nbsp;      1      &nb= sp;      0       = ; 0.824466   -3.180313    0.000000
   = 11          1   =           0   &n= bsp;    1.945446   -0.919177    0.00= 0000
   12         = ; 1             = 0        3.398064   -0.242189&n= bsp;   0.000000
 -----------------------------------------= ----------------------------
 Rotational constants (GHZ):  = ;    3.6566956      1.7161673    &= nbsp; 1.1744164
 ********************************************= **************************
      &nb= sp;     Population analysis using the SCF density.
=
 *****************************************************************= *****
 Electronic spatial extent (au):  <R**2>=3D&nb= sp;  919.2008
 Charge=3D     0.0000 electrons=
 Dipole moment (field-independent basis, Debye):
  &nb= sp; X=3D     1.8028    Y=3D   = -0.6387    Z=3D     0.0000  Tot=3D = ;    1.9126
 Quadrupole moment (field-independent bas= is, Debye-Ang):
   XX=3D   -30.6350   YY=3D&nbs= p;   -7.6894   ZZ=3D   -26.4884
   = XY=3D    -5.0915   XZ=3D     0.0000=    YZ=3D     0.0000
 Traceless Quadrupol= e moment (field-independent basis, Debye-Ang):
   XX=3D &nbs= p;  -9.0307   YY=3D    13.9149   ZZ=3D&n= bsp;   -4.8841
   XY=3D    -5.0915   XZ=3D     0.0000   YZ=3D&nbs= p;    0.0000
 Octapole moment (field-independent basi= s, Debye-Ang**2):
  XXX=3D    53.7799  YYY=3D &= nbsp;  -7.6173  ZZZ=3D     0.0000  XYY=3D&nbs= p;    5.7536
  XXY=3D    -2.5321  X= XZ=3D     0.0000  XZZ=3D    -7.1177 = ; YZZ=3D     1.2264
  YYZ=3D    = 0.0000  XYZ=3D     0.0000
 Hexadecapole mome= nt (field-independent basis, Debye-Ang**3):
 XXXX=3D  -509.3830 Y= YYY=3D  -156.7525 ZZZZ=3D   -23.2511 XXXY=3D    30.6= 051
 XXXZ=3D     0.0000 YYYX=3D    48= .4794 YYYZ=3D     0.0000 ZZZX=3D     0.0= 000
 ZZZY=3D     0.0000 XXYY=3D  -160.2397 XXZZ=3D   -90.8949 YYZZ=3D   -82.457= 0
 XXYZ=3D     0.0000 YYXZ=3D    = ; 0.0000 ZZXY=3D    26.3538
 Atom   7 needs v= ariable   8=3D   0.9744477035 but is    0.9= 720898606
 Input z-matrix variables are not compatible with final st= ructure.

 FAULTILY FAULTLESS, ICILY REGULAR, SPLENDIDLY N= ULL...
           MAUDE= BY TENNYSON
 Error termination request processed by link 9999.
&= nbsp;Error termination via Lnk1e in C:\G03W\l9999.exe at Thu Nov 04 19:09:35= 2010.
 Job cpu time:  0 days  1 hours 13 minutes 15.0 sec= onds.
 File lengths (MBytes):  RWF=3D     20 = Int=3D      0 D2E=3D      0 Ch= k=3D     11 Scr=3D      1
=
 Any insight would be very helpful.

 Thanks= !


=





--B_3377159158_4108613-- From owner-chemistry@ccl.net Thu Jan 6 09:49:00 2011 From: "Alex A Granovsky gran%x%classic.chem.msu.su" To: CCL Subject: CCL: CUDA/Linux security hole Message-Id: <-43537-110106091645-2905-rj5zPdTk2MIxX34XXBHuwg%a%server.ccl.net> X-Original-From: "Alex A Granovsky" Date: Thu, 6 Jan 2011 09:16:43 -0500 Sent to CCL by: "Alex A Granovsky" [gran(!)classic.chem.msu.su] Dear CCLers, I'd ask you to draw your attention to the two recent posts on the Firefly's QC discussion forum: http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/? C35e9ea936bHW-7675-1380-00.htm http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/? C35e9ea936bHW-7676-1022+00.htm The reason is not the Firefly package itself, nor it is the announce of availability of Linux/CUDA enabled Firefly version. The actual reason is the very important security hole we found a couple of days ago in Linux CUDA drivers. This hole is described in two posts mentioned above, and the only available workaround we know right now is to completely disable CUDA drivers on all multi-user Linux systems and clusters. Kind regards, Alex Granovsky, Firefly Project. From owner-chemistry@ccl.net Thu Jan 6 10:37:00 2011 From: "Iain Moal Iain.Moal=-=cancer.org.uk" To: CCL Subject: CCL: reforming a crystal dimer Message-Id: <-43538-110106082407-12044-7KoGQUUVCjowDJh1OzMCtA~~server.ccl.net> X-Original-From: Iain Moal Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Jan 2011 13:23:45 +0000 MIME-Version: 1.0 Sent to CCL by: Iain Moal [Iain.Moal : cancer.org.uk] Usually you can download the biological assembly from the protein databank. Iain ________________________________________ > From: owner-chemistry+iain.moal==cancer.org.uk/./ccl.net [owner-chemistry+iain.moal==cancer.org.uk/./ccl.net] On Behalf Of Vishal Handa vishal.kohli]|[hotmail.com [owner-chemistry/./ccl.net] Sent: 06 January 2011 11:18 To: Iain Moal Subject: CCL: reforming a crystal dimer Sent to CCL by: "Vishal Handa" [vishal.kohli**hotmail.com] Hi, was wondering if anyone could help me reform a crystal dimer from its monomer, any help would be greatly appreciated thanks Vishalhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. From owner-chemistry@ccl.net Thu Jan 6 11:29:00 2011 From: "Ivanciuc, Ovidiu I. oiivanci---utmb.edu" To: CCL Subject: CCL: Metalloorganic modeling Message-Id: <-43539-110106112607-26750-2wsPTNjnNjOuiRYHUeIXmg .. server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Jan 2011 10:25:54 -0600 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci-#-utmb.edu] Adam, >>I was trying to obtain electrotopologic descriptors for a 3D-QSAR model of a set of organopalladates If you try to compute Kier-Hall Electrotopological State (E-state) indices, you need only the molecular graph. For E-state field indices used in 3D-QSAR you need an approximate geometry that may be obtained with MM+ in Hyperchem, and the E-state field indices may be computed with Molconn-Z. For E-state field indices, in the standard Kier-Hall definition, you don't need atomic charges. O. ________________________________________ > From: owner-chemistry+oiivanci==utmb.edu#%#ccl.net [owner-chemistry+oiivanci==utmb.edu#%#ccl.net] On Behalf Of Adam Mark Vogt aavogt : ymail.com [owner-chemistry#%#ccl.net] Sent: Wednesday, January 05, 2011 9:10 PM To: Ivanciuc, Ovidiu I. Subject: CCL: Metalloorganic modeling Sent to CCL by: "Adam Mark Vogt" [aavogt[A]ymail.com] I was trying to obtain electrotopologic descriptors for a 3D-QSAR model of a set of organopalladates, and it showed that nothing of the available forcefields (at least that I know of) are not parametrized for transition metals (in my case; palladium). So, I tried to conduct semi-empirical as well as ab initio calculations to calculate point charges using hyperchem, yet regardless of the basis set or method, an error message about the atomic number being not supported always comes out. My questions is, is there some method to successfully simulate the electronic environment at the metal core and its surrounding? Thanks in Advance, Adam Vogt.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 Thu Jan 6 14:05:00 2011 From: "david.anick###rcn.com" To: CCL Subject: CCL:G: help Message-Id: <-43540-110106121626-19871-mftjc8BDWH/BhG7dMFkxZA*server.ccl.net> X-Original-From: Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 6 Jan 2011 12:16:15 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: [david.anick++rcn.com] Dear Bilel (or whoever started this thread), I work in the area of water clusters and I no longer use Gaussian but when I was using Gaussian I often got the problem of oscillating geometries UNTIL I started adding more internal coordinates via the MODREDUNDANT command. I found it necessary to add an internal coordinate for every H - - O hydrogen bond, at least. Convergence was better still if I included the O -- O distances for H- bonded pairs as well, and it helped even more to include angles and dihedrals that involved the H - - O "bonds". My MODREDUNDANT sections were much longer than the rest of the input combined. Your input line includes the word "modredundant" but you don't actually show which redundant coordinates you added. Try expanding these as above, and I think you will obtain rapid convergence to the optimum geometry. If that does not do it, then the problem is with the ULTRAFIN grid -- what happens if you do not use ULTRAFIN? Peace, David Anick PhD MD Harvard Medical School ---- Original message ---- >Date: Thu, 06 Jan 2011 11:45:55 +0100 >From: owner-chemistry+david.anick==rcn.com%x%ccl.net (on behalf of "Soren Eustis soreneustis]^[gmail.com" ) >Subject: CCL:G: help >To: "Anick, David " > > Greetings. The issue here is that the number of > optimization steps is exceeded. Gaussian has a > built in maximum that is predetermined from the size > (number if redundant internal coordinates) of the > system under study. Therefore, if you ask for > maxcycles=999 and the built in limit for a two water > system works out to be 100 - the run will stop after > 100 cycles. This is not all that unusual with a vdW > system like a water dimer. You can look at the > energies and forces for each step and see whether > they are steadily approaching their limits or if > they are oscillating around a shallow potential > well. In either case, I would take the final (step > 100) geometry and start a new calculation from > there. Use the opt(maxcycles=100, maxstep=10) > keywords. The latter is what will allow convergence > as Gaussian is likely making optimization steps that > are too large for such a shallow well. Secondly, I > would always use some extra diffuse functions for a > non-covalently bonded complex. > > If this does not work, there are a few other tricks > you can play with to find the minima. Gaussian's > online manual has more information > (http://www.gaussian.com/g_tech/g_ur/k_opt.htm) > > Regards, > > Soren > > -- > Soren N. Eustis, Ph.D. > ETH - Zurich > Environmental Organic Chemistry Group > Institute for Biogeochemistry and Pollutant Dynamics > Universitatstrasse 16 > CHN F33 > 8092 Zurich > > +41 44 632 93 48 (office) > +41 44 632 14 38 (fax) > > soren . env.ethz.ch > > From: "Delwar Hossain hossaind2004+*+yahoo.com" > > Reply-To: Ccl > Date: Wed, 5 Jan 2011 08:25:16 -0800 (PST) > To: Soren Eustis > Subject: CCL:G: help > Increase number of optimization step. If water > molecule is oscillating back and forth in a very > shallow potential energy surface, using CalcFC (or > SCF=QC) may help. > Thanks, > Delwar > > ------------------------------------------------ > > From: "Bilel Mansouri bilelmansouri80-,-yahoo.fr" > > To: "Hossain, Delwar " > Sent: Tue, January 4, 2011 11:51:53 AM > Subject: CCL:G: help > > HI > > I'm doing a (what I thought was simple) test job of tow water molecules whith > supermolecule methode using B3LYP > and I use the following input job > # opt=(modredundant,maxcycles=999), Int(Grid=ULTRAFIN) B3LYP/6- 311g > g counterpoise=2 > I have the error message and i use the keyword int=grid=ultrafine > > > Item Value Threshold Converged? > Maximum Force 0.000882 0.000450 NO > RMS Force 0.000269 0.000300 NO > > Maximum Displacement 0.056470 0.001800 NO > RMS Displacement 0.014132 0.001200 NO > Predicted change in Energy=-1.659919D-03 > Optimization stopped. From owner-chemistry@ccl.net Thu Jan 6 15:15:00 2011 From: "Adam Tenderholt atenderholt(_)gmail.com" To: CCL Subject: CCL:G: modifysph input help Message-Id: <-43541-110106151401-17919-JPYcouHcfoDsO0iPV6jDKg]=[server.ccl.net> X-Original-From: "Adam Tenderholt" Date: Thu, 6 Jan 2011 15:14:00 -0500 Sent to CCL by: "Adam Tenderholt" [atenderholt]^[gmail.com] Hi CCL, I'm trying to use Gaussian (03 or 09) to calculate a couple of solvation free energies. I want to check the effect of modifying the sphere radii for a couple of key atoms that I think may not be well-represented in the test sets used to parametrize default radii. I want to use the SMD-Couloumb radii for the rest of the atoms. So far, I have SCRF=(SMD,Solvent=CH3CN,Read) and the following lines in my input file (to say change spheres centered on atoms 1 and 2): modifysph 1 1.700 1.200 2 1.500 1.000 My output file shows the following, which makes me think that these spheres are not being modified correctly: .. Using the following non-standard input for PCM: modifysph --- end of non-standard input. Reading user-defined spheres from input: ISph on Nord Re0 Alpha Xe Ye Ze --- end of user-defined spheres data. .. Any suggestions? I also noticed that in some of my previous calculations, the sphere list gets printed but that is no longer the case. Is there a keyword I'm missing to make this listed get printed? Thanks, Adam -- Adam Tenderholt Research Associate Mayer Research Group University of Washington From owner-chemistry@ccl.net Thu Jan 6 22:54:00 2011 From: "Mahmoud A. A. Ibrahim m.ibrahim%x%compchem.net" To: CCL Subject: CCL:G: modifysph input help Message-Id: <-43542-110106224837-9782-WU7lPJ0vdk0WrVVZbBebtg]=[server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 7 Jan 2011 03:48:24 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim*|*compchem.net] Dear Adam It works without any problem. You have just checked the wrong line. The modified spheres' parameters will be found after the following line (comes below: Polarizable Continuum Model (PCM) table) ------------------------------------------------------------------------------ Spheres list: ISph on Nord Re0 Alpha Xe Ye Ze 1 O 1 1.700 1.200 0.000000 0.000000 0.448524 ------------------------------------------------------------------------------ Sincerely; M. Ibrahim On Thu, Jan 6, 2011 at 8:14 PM, Adam Tenderholt atenderholt(_)gmail.com wrote: > > Sent to CCL by: "Adam  Tenderholt" [atenderholt]^[gmail.com] > Hi CCL, > > I'm trying to use Gaussian (03 or 09) to calculate a couple of solvation free energies. I want to check the effect of modifying the sphere radii for a couple of key atoms that I think may not be well-represented in the test sets used to parametrize default radii. I want to use the SMD-Couloumb radii for the rest of the atoms. > > So far, I have SCRF=(SMD,Solvent=CH3CN,Read) and the following lines in my input file (to say change spheres centered on atoms 1 and 2): > > modifysph > >   1    1.700   1.200 >   2    1.500   1.000 > > My output file shows the following, which makes me think that these spheres are not being modified correctly: > > .. > Using the following non-standard input for PCM: >  modifysph >  --- end of non-standard input. >  Reading user-defined spheres from input: >  ISph  on   Nord    Re0     Alpha      Xe            Ye            Ze >  --- end of user-defined spheres data. > .. > > Any suggestions? I also noticed that in some of my previous calculations, the sphere list gets printed but that is no longer the case. Is there a keyword I'm missing to make this listed get printed? > > Thanks, > > Adam > > -- > Adam Tenderholt > Research Associate > Mayer Research Group > University of Washington>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > --                   Mahmoud A. A. Ibrahim                        Current Address                  7.05, School of Chemistry,               The University of Manchester,          Oxford Road, Manchester, M13 9PL,                        United Kingdom.                         Home Address                   Chemistry Department,                      Faculty of Science,                         Minia University,                            Minia 61519,                                 Egypt.                      Contact Information            Email: m.ibrahim::compchem.net               Website: www.compchem.net                    Fax No.: +20862342601