From owner-chemistry@ccl.net Tue Jun 16 07:09:01 2009 From: "aneesh cna aneeshcna.^.gmail.com" To: CCL Subject: CCL: Force constant calculation Message-Id: <-39527-090616070725-9446-EUHSIZJ0NH8yFYOKuZpMkA^server.ccl.net> X-Original-From: "aneesh cna" Date: Tue, 16 Jun 2009 07:07:21 -0400 Sent to CCL by: "aneesh cna" [aneeshcna]-[gmail.com] Can anyone help me clearing some doubts in force constant calculation using Gussian package. I did a frequency calculation for water molecule (as a trial) and force constant in Cartesian as well as internal coordinates from the output is give below.. ***************************************************************************** Force constants in Cartesian coordinates: 1 2 3 4 5 1 0.615710D+00 2 0.000000D+00 0.121662D-03 3 -0.126839D+00 0.000000D+00 0.705542D+00 4 -0.609095D-01 0.000000D+00 -0.588957D-01 0.573191D-01 5 0.000000D+00 -0.608311D-04 0.000000D+00 0.000000D+00 0.418506D-04 6 0.108386D-01 0.000000D+00 -0.599717D+00 -0.152672D-03 0.000000D+00 7 -0.554801D+00 0.000000D+00 0.185735D+00 0.359039D-02 0.000000D+00 8 0.000000D+00 -0.608311D-04 0.000000D+00 0.000000D+00 0.189806D-04 9 0.116000D+00 0.000000D+00 -0.105826D+00 0.590483D-01 0.000000D+00 6 7 8 9 6 0.613253D+00 7 -0.106860D-01 0.551210D+00 8 0.000000D+00 0.000000D+00 0.418506D-04 9 -0.135356D-01 -0.175049D+00 0.000000D+00 0.119361D+00 Force constants in internal coordinates: 1 2 3 1 0.612864D+00 2 -0.636590D-02 0.612864D+00 3 0.262746D-01 0.262746D-01 0.184953D+00 *************************************************************************************** How can I get the force constant for bond stretching and angle bending ( here O-H bond and H-O-H bending) from this force constant matrix?.Can anyone help me in figure out this problem. waiting for your valuable reply Thanks in advance Aneesh aneeshcna(!)gmail.com From owner-chemistry@ccl.net Tue Jun 16 07:50:01 2009 From: "Adil Zhugralin zhugrali**bc.edu" To: CCL Subject: CCL:G: Gaussian03 error in generating .wfn file Message-Id: <-39528-090616074851-11421-c2sqHY18CXdcLDgThnYs2w{}server.ccl.net> X-Original-From: "Adil Zhugralin" Date: Tue, 16 Jun 2009 07:48:48 -0400 Sent to CCL by: "Adil Zhugralin" [zhugrali _ bc.edu] Dear CCL'ers: In my attempts to generate a MP2 wavefunction with the input: # mp2(full)/gen 6D 10F density=current output=wfn geom=connectivity scf(xqc,tight) int=grid=ultrafine maxdisk=100GB .mol specs, etc... n12.wfn I got an empty .wfn file. The .log file on the other hand shows that MP2 wavefunction generation went well (Population analysis of MP2 densities is there with all the natural orbitals, etc.) However, the file ends with the following error: Writing a WFN file to n12.wfn. IPrim.ne.NPrim in ShlToP. Error termination via Lnk1e in /usr/public/gaussian/g03.e01/l9999.exe at Tue Jun 16 01:45:56 2009. Job cpu time: 0 days 7 hours 42 minutes 35.6 seconds. File lengths (MBytes): RWF= 93104 Int= 0 D2E= 0 Chk= 40 Scr= 1 What does this error mean? How do I get around it, considering that everything up to writing a .wfn file seems to be fine? Thanks in advance. Adil From owner-chemistry@ccl.net Tue Jun 16 09:06:01 2009 From: "Pedro Silva pedros%a%ufp.pt" To: CCL Subject: CCL: Energies in spin-contaminated functions acc Ovchinnikov and Labanowski Message-Id: <-39529-090615202400-25939-BZWyLOHRPeRRpDR5s1aEIQ.:.server.ccl.net> X-Original-From: "Pedro Silva" Date: Mon, 15 Jun 2009 20:23:57 -0400 Sent to CCL by: "Pedro Silva" [pedros- -ufp.pt] Dear CCL-list members, I have a doublet wave-function contaminated with the quadruplet and sectuplet states. According to Ovchinnikov and Labanowski(1996)Physical Review A ,53,3946 one can obtain the corrected energy for the pure doublet by solving a system of equations described in its page 3950. In order to solve this system, one must compute a series of values (defined in a formula from the previous pages). Does any one know whether any program for these computations has ever been made available by the authors? Thanks for any help, Pedro From owner-chemistry@ccl.net Tue Jun 16 10:30:00 2009 From: "Jim Kress ccl_nospam,kressworks.com" To: CCL Subject: CCL: Question about GAMESS/TINKER - no link atoms Message-Id: <-39530-090616084858-2043-NQqOexXrVhkSOhmGQn1dzw^^server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 16 Jun 2009 08:42:26 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam---kressworks.com] Did you try to run it or is this a purely hypothetical question? I'd suggest you try to run your test case and see what happens. Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com|-|ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com|-|ccl.net] > On Behalf Of Shahar Keinan skeinan*_*gmail.com > Sent: Monday, June 15, 2009 10:51 AM > To: Kress, Jim > Subject: CCL: Question about GAMESS/TINKER - no link atoms > > > Sent to CCL by: "Shahar Keinan" [skeinan^gmail.com] Dear all, > > I have submitted this question about a week ago, and have not > heard anything back. I have also submitted this question to > the GAMESS forum, with no reply. I am trying again. > > I am trying to do a QM/MM calculation with GAMESS/TINKER, > however, I want to run the calculations without link atoms. > Is this possible? > The example files all have link atoms in them. > > Thank you, > Dr. Shahar Keinan > Duke University > > > I am attaching an example of an input file that gets an error > message (this is a water dimer, one water molecule QM, the > other TIP3): > > ! An example file to perform > ! QM/MM. > ! water dimer, no link atoms. One water is TIP3, ! other > water described with HF/STO-3G ! > $CONTRL SCFTYP=RHF RUNTYP=optimize COORD=UNIQUE NZVAR=33 > $END $BASIS GBASIS=sto NGAUSS=3 $END > $ZMAT DLC=.T. AUTO=.T. $END > $DATA > Ab initio atoms in QM region > C1 > O 8.0 -0.032947 0.000000 0.005966 > H 1.0 0.270601 0.000000 0.911928 > H 1.0 0.792970 0.000000 -0.510216 > $END > $LINK IMOMM=.T. IQMATM(1)=1,2,3 $END > $TINKEY > parameters /home/skeinan/gamess_tinker/tinker/params/charmm > $END > $TINXYZ > 6 water dimer > 1 OT -0.032947 0.000000 0.005966 91 2 3 > 2 HT 0.270601 0.000000 0.911928 83 1 > 3 HT 0.792970 0.000000 -0.510216 83 1 > 4 HT 2.756636 0.756897 -1.740089 83 5 > 5 OT 2.373120 0.000000 -1.290448 91 4 6 > 6 HT 2.756636 -0.756897 -1.740089 83 5 > $END > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the |-| sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Tue Jun 16 11:05:00 2009 From: "Nuno A. G. Bandeira nuno.bandeira]-[ist.utl.pt" To: CCL Subject: CCL: Energies in spin-contaminated functions acc Ovchinnikov and Labanowski Message-Id: <-39531-090616105742-3864-MJHR9TE2ze2CdY2EbeVBug*server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 16 Jun 2009 15:57:25 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira]![ist.utl.pt] Pedro Silva pedros%a%ufp.pt wrote: > Sent to CCL by: "Pedro Silva" [pedros- -ufp.pt] > Dear CCL-list members, > > I have a doublet wave-function contaminated with the quadruplet and sectuplet states. According to > Ovchinnikov and Labanowski(1996)Physical Review A ,53,3946 > one can obtain the corrected energy for the pure doublet by solving a system of equations described in its page 3950. In order to solve this system, one must compute a series of values (defined in a formula from the previous pages). Does any one know whether any program for these computations has ever been made available by the authors? > > Thanks for any help, Assuming you're using DFT you can look up the broken spin (BS) and spin projection literature on this subject. Starting from Noodleman et al to Yamaguchi and recent pedagogic reviews by Eliseo Ruiz are good sources to refer to. DFT is usually not plagued with spin contamination unless you purposefully contaminate the wavefunction (such as in the BS technique). Cheers, Nuno -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student .*. IST,Lisbon -- From owner-chemistry@ccl.net Tue Jun 16 11:40:00 2009 From: "Alain Borel alain.borel~~epfl.ch" To: CCL Subject: CCL: pKa data base... Message-Id: <-39532-090616084750-1928-FA0b0RqRbeMADKOVT1Kp7w]=[server.ccl.net> X-Original-From: Alain Borel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 16 Jun 2009 07:41:00 +0200 MIME-Version: 1.0 Sent to CCL by: Alain Borel [alain.borel- -epfl.ch] S. Bill S_Bill36=yahoo.co.uk wrote: > I was wondering if there is a data base for pKa values for ligands. The IUPAC Stability Constants Database (http://www.acadsoft.co.uk/) contains stability constants for tens of thousands of ion/ligand pairs... H+ is just one particular ion. Cheers, Alain Borel Bibliothèque Scientifique Commune UNIL-EPFL BCH 2201 EPFL - SB - SCGC-BCH 1015 Lausanne, Switzerland. Tel.: +41 21 693 9800 Fax.: +41 21 693 9805 e-mail: alain.borel() epfl.ch http://biscom.epfl.ch From owner-chemistry@ccl.net Tue Jun 16 14:01:00 2009 From: "Pedro Silva pedros|a|ufp.pt" To: CCL Subject: CCL: Energies in spin-contaminated functions acc Ovchinnikov and Labanowski Message-Id: <-39533-090616135928-4629-nZPh83krMJWY1PEv6XWyNQ]=[server.ccl.net> X-Original-From: "Pedro Silva" Date: Tue, 16 Jun 2009 13:59:24 -0400 Sent to CCL by: "Pedro Silva" [pedros{}ufp.pt] Dear Nuno, Thanks for your suggestion about the Broken symmetry approach: As it happens, I had just downloaded the Noodleman paper this morning, and started the sextuplet computations (the quadruplet was still contaminated, so that I have to compute the next-lower pure spin state. I hope I do not have to compute the octuplet too :-) Regarding DFT, I am indeed aware that DFT is not as plagued by spin-contamination, but I need to perform my computations with MP2: the referees were not completely convinced by my use of DFT to compute gas-phase redox potentials. Thanks again! Pedro From owner-chemistry@ccl.net Tue Jun 16 15:18:01 2009 From: "Shahar Keinan skeinan],[gmail.com" To: CCL Subject: CCL: Question about GAMESS/TINKER - no link atoms Message-Id: <-39534-090616151603-14284-A66yDsMjOIy3+3674TvTkA#server.ccl.net> X-Original-From: Shahar Keinan Content-Type: multipart/alternative; boundary=001636c5a826851c5c046c7b8ec1 Date: Tue, 16 Jun 2009 14:43:54 -0400 MIME-Version: 1.0 Sent to CCL by: Shahar Keinan [skeinan~!~gmail.com] --001636c5a826851c5c046c7b8ec1 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Jim, I did try this, and got the following error message: .... Parameter file unit number 1 *** TINKER INTIALIZATION COMPLETE *** ---- QMMM procedure is ON ---- LINKING ATOM PAIRS ------------------ NO QM-ATOM MM-ATOM *** ERROR IN LINK SPECIFICATION *** QMMM REQUIRES at least one Linkge .... Best, Shahar On Tue, Jun 16, 2009 at 8:42 AM, Jim Kress ccl_nospam,kressworks.com < owner-chemistry]|[ccl.net> wrote: > > Sent to CCL by: "Jim Kress" [ccl_nospam---kressworks.com] > Did you try to run it or is this a purely hypothetical question? > > I'd suggest you try to run your test case and see what happens. > > Jim > > > -----Original Message----- > > From: owner-chemistry+ccl_nospam==kressworks.com+*+ccl.net > > [mailto:owner-chemistry+ccl_nospam == > kressworks.com+*+ccl.net] > > On Behalf Of Shahar Keinan skeinan*_*gmail.com > > Sent: Monday, June 15, 2009 10:51 AM > > To: Kress, Jim > > Subject: CCL: Question about GAMESS/TINKER - no link atoms > > > > > > Sent to CCL by: "Shahar Keinan" [skeinan^gmail.com] Dear all, > > > > I have submitted this question about a week ago, and have not > > heard anything back. I have also submitted this question to > > the GAMESS forum, with no reply. I am trying again. > > > > I am trying to do a QM/MM calculation with GAMESS/TINKER, > > however, I want to run the calculations without link atoms. > > Is this possible? > > The example files all have link atoms in them. > > > > Thank you, > > Dr. Shahar Keinan > > Duke University > > > > > > I am attaching an example of an input file that gets an error > > message (this is a water dimer, one water molecule QM, the > > other TIP3): > > > > ! An example file to perform > > ! QM/MM. > > ! water dimer, no link atoms. One water is TIP3, ! other > > water described with HF/STO-3G ! > > $CONTRL SCFTYP=RHF RUNTYP=optimize COORD=UNIQUE NZVAR=33 > > $END $BASIS GBASIS=sto NGAUSS=3 $END > > $ZMAT DLC=.T. AUTO=.T. $END > > $DATA > > Ab initio atoms in QM region > > C1 > > O 8.0 -0.032947 0.000000 0.005966 > > H 1.0 0.270601 0.000000 0.911928 > > H 1.0 0.792970 0.000000 -0.510216 > > $END > > $LINK IMOMM=.T. IQMATM(1)=1,2,3 $END > > $TINKEY > > parameters /home/skeinan/gamess_tinker/tinker/params/charmm > > $END > > $TINXYZ > > 6 water dimer > > 1 OT -0.032947 0.000000 0.005966 91 2 3 > > 2 HT 0.270601 0.000000 0.911928 83 1 > > 3 HT 0.792970 0.000000 -0.510216 83 1 > > 4 HT 2.756636 0.756897 -1.740089 83 5 > > 5 OT 2.373120 0.000000 -1.290448 91 4 6 > > 6 HT 2.756636 -0.756897 -1.740089 83 5 > > $END > > > > > > > > -= This is automatically added to each message by the mailing > > script =- To recover the email address of the author of the > > message, please change the strange characters on the top line > > to the +*+ sign. You can also look up the X-Original-From: line > > in the mail header.> Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/> > > --001636c5a826851c5c046c7b8ec1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Jim,

I did try this, and got the following error message:
..= ..
Parameter file unit number=A0=A0=A0 1
=A0=A0=A0=A0=A0 *** TINKER I= NTIALIZATION COMPLETE ***
=A0
=A0---- QMMM procedure is ON ----
=A0=A0=A0=A0=A0=A0=A0=A0=A0 LINKING ATOM PAIRS
=A0=A0=A0=A0=A0=A0=A0=A0=A0 ------------------
=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 NO=A0=A0=A0 QM-ATOM=A0=A0=A0 MM-ATOM
=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 *** ERROR IN LINK SPECIFICATION ***
=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 QMMM REQUIRES at least one Linkge
....

Best,
Shahar


On Tue, Jun 16, 2009 at 8:42 AM, Jim Kress ccl_n= ospam,kressworks.com <owner-chemistry]|[ccl.net> wrote:

Sent to CCL by: "Jim Kress" [ccl_nospam---kressworks.com]
Did you try to run it or is this a purely hypothetical question?

I'd suggest you try to run your test case and see what happens.

Jim

> -----Original Message-----
> From: owner-chemistry+ccl_nospam=3D=3Dkressworks.com+*+ccl.net
> [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com+*+ccl.net]
> On Behalf Of Shahar Keinan skeinan*_*gmail.com
> Sent: Monday, June 15, 2009 10:51 AM
> To: Kress, Jim
> Subject: CCL: Question about GAMESS/TINKER - no link atoms
>
>
> Sent to CCL by: "Shahar =A0Keinan" [skeinan^gmail.com] Dear all,
>
> I have submitted this question about a week ago, and have not
> heard anything back. I have also submitted this question to
> the GAMESS forum, with no reply. I am trying again.
>
> I am trying to do a QM/MM calculation with GAMESS/TINKER,
> however, I want to run the calculations without link atoms.
> Is this possible?
> The example files all have link atoms in them.
>
> Thank you,
> Dr. Shahar Keinan
> Duke University
>
>
> I am attaching an example of an input file that gets an error
> message (this is =A0a water dimer, one water molecule QM, the
> other TIP3):
>
> ! =A0An example file to perform
> ! =A0QM/MM.
> ! =A0water dimer, no link atoms. One water is TIP3, ! =A0other
> water described with HF/STO-3G !
> =A0$CONTRL SCFTYP=3DRHF RUNTYP=3Doptimize COORD=3DUNIQUE NZVAR=3D33 > $END =A0$BASIS =A0GBASIS=3Dsto NGAUSS=3D3 =A0$END
> =A0$ZMAT =A0 DLC=3D.T. AUTO=3D.T. $END
> =A0$DATA
> Ab initio atoms in QM region
> C1
> O =A0 =A0 =A0 =A0 =A0 8.0 =A0-0.032947 =A0 =A0 =A0 0.000000 =A0 =A0 = =A0 0.005966
> H =A0 =A0 =A0 =A0 =A0 1.0 =A0 0.270601 =A0 =A0 =A0 0.000000 =A0 =A0 = =A0 0.911928
> H =A0 =A0 =A0 =A0 =A0 1.0 =A0 0.792970 =A0 =A0 =A0 0.000000 =A0 =A0 = =A0-0.510216
> =A0$END
> =A0$LINK IMOMM=3D.T. IQMATM(1)=3D1,2,3 $END
> =A0$TINKEY
> parameters /home/skeinan/gamess_tinker/tinker/params/charmm
> =A0$END
> =A0$TINXYZ
> 6 =A0water dimer
> 1 =A0OT =A0-0.032947 =A0 =A00.000000 =A0 =A00.005966 =A091 =A0 =A0 2 = =A0 =A0 3
> 2 =A0HT =A0 0.270601 =A0 =A00.000000 =A0 =A00.911928 =A083 =A0 =A0 1 > 3 =A0HT =A0 0.792970 =A0 =A00.000000 =A0 -0.510216 =A083 =A0 =A0 1
> 4 =A0HT =A0 2.756636 =A0 =A00.756897 =A0 -1.740089 =A083 =A0 =A0 5
> 5 =A0OT =A0 2.373120 =A0 =A00.000000 =A0 -1.290448 =A091 =A0 =A0 4 =A0= =A0 6
> 6 =A0HT =A0 2.756636 =A0 -0.756897 =A0 -1.740089 =A083 =A0 =A0 5
> =A0$END
>
>
>
> -=3D This is automatically added to each message by the mailing
> script =3D- To recover the email address of the author of the
> message, please change the strange characters on the top line
> to the +*+ sign. You can also look up the X-Original-From: line
> in the mail header.> Conferences:
> http://server.ccl.net/chemistry/announcements/conference= s/>
>



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--001636c5a826851c5c046c7b8ec1-- From owner-chemistry@ccl.net Tue Jun 16 22:10:00 2009 From: "Jan Labanowski janl-x-speakeasy.net" To: CCL Subject: CCL: Energies in spin-contaminated functions acc Ovchinnikov and Labanowski Message-Id: <-39535-090616220652-29097-7jb4iJb3bU5U1Mj7msU9vw-,-server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 16 Jun 2009 22:06:43 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl[a]speakeasy.net] Dear Pedro, You asked about the code to a method described in Ovchinnikov and Labanowski(1996)Physical Review A ,53,3946. Unfortunately, no code survived... The method was programmed on the top of some well known DFT package at that time. However, the code was in the proc= ess of commercialization and we could not just redistribute the source. Moreove= r, other priorities did not allow us to spend more time and create some sensib= le "plug-in" into other codes or create "Yet Another Quantum Chemistry Package" so we could avoid dependence on other peoples software. More computational details and actual algorithms used were described in: Ovchinnikov A.A., Bender C.F., Labanowski J.K.: A Simple Method of Removing Spin Contamination from Unrestricted Kohn-Sham Density Functional Calculations. In: Recent Developments and Applications of Modern Density Functional Theory. (Theor. and Comput. Chem., vol. 4) J.M. Seminario, (Ed.), pp. 359-388, Elsevier, Amsterdam, (1996). I "do not do science" any more and the other coauthors joined the Angels in Heaven, so it is hard to say if the method will actually be reimplemented even though results were extremely promising. Jan