From owner-chemistry@ccl.net Wed Jun 13 04:00:00 2007 From: "Frank Neese neese:thch.uni-bonn.de" To: CCL Subject: CCL: ORCA and ECP basis sets Message-Id: <-34468-070613035756-9882-B6iIRa4vPvLxYAGv1Hxl9Q*server.ccl.net> X-Original-From: Frank Neese Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Wed, 13 Jun 2007 09:57:47 +0200 Mime-Version: 1.0 Sent to CCL by: Frank Neese [neese-,-thch.uni-bonn.de] Dear Chad, unfortunately, ECP's are not yet available in ORCA. Since we have realized that this is a serious shortcoming, we are presently working on it and there is some hope that it becomes available in the late summer or autmun. At this point, geometry optimizations for gold containing clusters are only possible with a scalar relativistic all electron approach which is, of course, much more expensive than the ECP calculations. Once the ECP's become available in ORCA we will likely follow the GAMESS US format in EMSL since we have all other basis input in this format. The problems with the mailing list are acknowledged and should be corrected in the near future. With my best regards, Frank Neese From owner-chemistry@ccl.net Wed Jun 13 05:41:01 2007 From: "Jos I. Garc a jig[a]unizar.es" To: CCL Subject: CCL: Negative frequency problem Message-Id: <-34469-070613033758-8901-ubKBCpHyTvdU1vpIxYHHBA^server.ccl.net> X-Original-From: "Jos I. Garc a" Date: Wed, 13 Jun 2007 03:37:54 -0400 Sent to CCL by: "Jos I. Garc a" [jig _ unizar.es] Hi Gary, If your system and/or your computational resources allow it, try the old, but usually effective OPT=(TS,CalcAll,...). A second, small, negative frequency, associated to a low-energy torsion is really a pain in the neck, and if we could simply ignore it, it would be great. However, try to eliminate it first. You'll feel better after... Jos I. Garca CSIC Research Professor Instituto de Ciencia de Materiales de Aragon CSIC-Universidad de Zaragoza E-50009 Zaragoza (Spain) From owner-chemistry@ccl.net Wed Jun 13 07:08:01 2007 From: "Wai-To Chan chan!=!curl.gkcl.yorku.ca" To: CCL Subject: CCL:G: Limitations of DFT Message-Id: <-34470-070613070011-1896-z38te6PgSimckAwtuRMc5w(-)server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 13 Jun 2007 07:45:14 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan++curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< However, one of the reviewers on *this* manuscript objected to the use of the DFT calculations with the following: "With regards to using DFT calculations to distinguish between mechanisms B and C, I would put no confidence in such a result. It is well known that DFT calculations greatly overemphasize the stabilization provided by delocalization, so they have a built-in bias towards concerted reactions, which is useful if the reaction actually is concerted, but a disaster if it is not." Is this a true statement? And, if so, where can I find more about this limitation of DFT theory? I have searched but come up empty so far. Plus, I'm not sure exactly what the reviewer means, since the diradical intermediate of mechanism C would also be subject to delocalization effects...possibly even greater than those expected by a "concerted" reaction! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I assume reaction pathway (B) proceeds via a TS characterized by spin-restricted (R)DFT, (C) a open-shell TS characterized by unrestricted DFT and the reactant is closed-shell and treated by RDFT. Did you check the wavefunction stability of the TS for (B)? Instability of RHF and/or RDFT is a telling sign of discontinuity within your PES. The theoretical foundation underlying the characterization of the kind of PES with stationary points of varying degree of diradical character using single-reference type of methods is shaky. I however don't see any relevance of your reviewer's remarks to the limiation of DFT. DFT indeed does suffer from wavefunction stability and its reliability for the prediction of concerted and stepwise mechanism involving diradicals is seldom addressed. But I never heard of any studies which demonstrate that DFT is biased towards the concerted pathway. I seem to remember that DFT has been applied to characterization of the aromaticity of transition state structures in concerted reaction mechanism through NICS calculations. I am not familiar with the literature in this area but I doubt very much one can draw any conclusion from such studies alone on DFT's favouring of the concerted mehanism in pericyclic reactions. If I were you I would demand the referee to provide a reference to back up his/her comments further. Chance is that the referee's comments are merely speculations rather than established facts. It is not just DFT. The entire specturm of commonly employed single-reference type of methods (HF, MPn, CCSD(T), DFT) is inherently problematic for a consistently accurate characterization of a diradical PES. CASSCF in principle could solve the problem arising > from PES discontinuity. In practice CASSCF won't necessarily give more accurate structural and energetic predictions than DFT. DFT has been applied to the study of concerted and stepwise mechansims in cycloaddition reaction for years. Occassionaly serious discrepancies between DFT and CASSCF were noted. But no one to my knowledge has suggested DFT should be avoided in favour of other methods in general. There are other promising alternatives to DFT for diradical PES outside GAUSSIAN. Unless these methods have already gained general acceptance and are applicable to the system you are studying you don't have the obligation to 'upgrade' your DFT calculations in my view. My advice for you is to come up with a cogent response to the questions of the referee. You should in your discussion of your results highlight those limitations of the theories employed and convince the readers that the computations were properly executed within the limitations. As long as you lay out the facts clearly to allow the readers to assess your results you should stand a reasonable chance of getting your work accepted. Wai-To Chan From owner-chemistry@ccl.net Wed Jun 13 08:42:01 2007 From: "Wolfgang Quapp quapp-*-rz.uni-leipzig.de" To: CCL Subject: CCL:G: Wilson B matrix in Gaussian Message-Id: <-34471-070613040238-11021-7eLbUZAueechymmo1cTGpA#,#server.ccl.net> X-Original-From: "Wolfgang Quapp" Date: Wed, 13 Jun 2007 04:02:35 -0400 Sent to CCL by: "Wolfgang Quapp" [quapp]*[rz.uni-leipzig.de] Dear ALL, I try to include Gaussian03 into a calculation of a reaction path. I have to use z-matrix coordinates (non redundant) of a given structure for the input. I need in the output file: energy, gradient, Hessian, and (non-massweighted) metric-matrix G, or the Wilson B-matrix in the given internal curvilinear coordinates being z-matrix-coordinates. I tested the IOp(1/33=2) or IOp(1/33=3) which gives a B matrix in "full" redundant coordinates, however, only 12 lines (?) for every sort of molecule. However, it does not include in the set of the "full" redundant coordinates all the pre-given z-matrix coordinates. Thats why, it is not possible, that I simple delete some lines of the "full" G-matrix because at least one internal coodinate of the given Z-matrix is missing in the so-called "full"-redundant internals. Because it is possible to obtain gradient and Hessian in the given Z-Matrix coordinates, using opt=(Z-Matrix,CALCALL), it has to be a procedure inside Gaussian which uses the true B-Matrix. Is there any possibility to get the desired values being an external user? With many thanks for your help in advance Wolfgang Quapp quapp a rz.uni-leipzig.de From owner-chemistry@ccl.net Wed Jun 13 09:17:01 2007 From: "littlecan p9894105%x%mail.ncku.edu.tw" To: CCL Subject: CCL: Problems about AMBER Message-Id: <-34472-070613031732-7095-BZWyLOHRPeRRpDR5s1aEIQ:+:server.ccl.net> X-Original-From: "littlecan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0013_01C7ADC9.A3E82400" Date: Wed, 13 Jun 2007 14:46:35 +0800 MIME-Version: 1.0 Sent to CCL by: "littlecan" [p9894105..mail.ncku.edu.tw] This is a multi-part message in MIME format. ------=_NextPart_000_0013_01C7ADC9.A3E82400 Content-Type: text/plain; charset="big5" Content-Transfer-Encoding: quoted-printable Dear Sir/Madam: =20 Recently, I started using AMBER and have encountered problems regarding = van der waals energy calculation. The protein (PDB:1L5G) consists of an integrin part and a RGD-containing = ligand (chain C), and the integrin part contains chains A and B. The C = atom of Arg in RGD, labeled as CZ atom type in PDB (ARG_5001 of C = chain), is a CA atom type in AMBER. We make the C atom of Arg in RGD the = center of a disk with 9 A radius, identify all atoms within the disk, = and try to calculate the van der waals energy term of AMBER (1995) = between the C atom of Arg in RGD and every identified atom, where the = 1-2 and 1-3 interactions are excluded. Then, we encountered the = following problems. 1. The van der waals energy calculated for some atom = pairs are positive, where the paired atoms may be either from the same = chain or from two different chains. For example, we calculated the van = der waals energy between the pair of HD2 atom of TYR_178 in A chain and = the CZ atom in ARG_5001 of C chain. As shown in the table below, the = 1995 Cornell model gives Ri* of HD2 atom to be 1.459 A, the Rj* of CZ is = 1.908 A, and the resultant Rij* is 3.367 A. From Cornell 1995,=A3`i =3D = 0.015 kcal/mol (van der waals well depth of HD2), =A3`j =3D 0.086 (van = der waals well depth of CZ), and we obtained Aij=3D 76245.16, = Bij=3D104.6607. Let Rij be the Euclidean distance between HD2 and CZ = atoms. We obtained Rij=3D1.88247 A by hand calculation and it is = confirmed using HyperChem. The van der waals energy is then calculated = to be 36.14942817 kcal/mole, quite a positive value. Similarly, we also = obtained a positive value of 2.77 kcal/mol as the van der waals energy = between HD2 atom of TYR_178 in A chain and NE atom of ARG_5001 in chain = C. We are not sure about either our calculation is incorrect or it is = reasonable to have positive van der waals energy in those cases. 2. In the 1995 paper by Cornell et al., the scale = factor of 1/2.0 is recommended for reducing the 1-4 VDW interactions as = used previously by Weiner et al. (lines 6 to 8 from the bottom of the = right-hand column in page 5183). Is our interpretation correct? =20 Tabled Values for TYR_178_A(HD2)(HA)-ARG_5001_C(CZ)(CA): Ri*=3D 1.459 Rj*=3D1.908 Rij*=3D 3.367 =A3`i =3D 0.015 =A3`j =3D 0.086 =A3`ij=3D(=A3`i=A3`j)^0.5=3D 0.035917 Aij=3D=A3`ij(Rij*)^12=3D 76245.16 Bij=3D2=A3`ij(Rij*)^6=3D 104.6607 Rij=3D 1.88247 Evdw=3DAij/(Rij^12)-Bij/(Rij^6)=3D 36.14942817 =20 We are looking forward to hearing from you. Your help in this respect is = highly appreciated. =20 Sincerely Yours,=20 Yu-hui Fang e-mail: p9894105{}ccmail.ncku.edu.tw =20 =20 ------=_NextPart_000_0013_01C7ADC9.A3E82400 Content-Type: text/html; charset="big5" Content-Transfer-Encoding: quoted-printable

Dear Sir/Madam:

 

Recently, I started = using AMBER=20 and have encountered problems regarding van der waals energy=20 calculation.

The protein=20 (PDB:1L5G) consists of an integrin part and a=20 RGD-containing ligand (chain C), and the integrin part contains chains A = and B.=20 The C atom of Arg in RGD, labeled as CZ atom type in PDB (ARG_5001 of C = chain),=20 is a CA atom type in AMBER. We make the C atom of Arg in RGD the center = of a=20 disk with 9 Å radius, identify all atoms within the disk, = and try to=20 calculate the van der waals energy term of AMBER (1995) between the C = atom of=20 Arg in RGD and every identified atom, where the 1-2 and 1-3 interactions = are=20 excluded. Then, we encountered the following = problems.

 

1.           = ;      =20 The van der waals = energy=20 calculated for some atom pairs are positive, where the paired atoms may = be=20 either from the same chain or from two different chains. For example, we = calculated the van der waals energy between the pair of HD2 atom of=20 TYR_178 = in A chain=20 and the CZ atom in ARG_5001 of C chain. As shown in the table below, the = 1995=20 Cornell model gives Ri* of HD2 atom to be 1.459 Å, the Rj* of CZ=20 is 1.908 = Å, and the resultant Rij* is = 3.367 Å.=20 From=20 Cornell 1995,=A3`i =3D 0.015 kcal/mol=20 (van der waals = well depth=20 of HD2),=20 =A3`j =3D 0.086 (van der waals well depth of = CZ),=20 and we obtained Aij=3D 76245.16, Bij=3D104.6607. Let Rij be the = Euclidean distance=20 between HD2 and CZ atoms. We obtained = Rij=3D1.88247 = Å by hand calculation = and it is=20 confirmed using HyperChem. The van der waals = energy is=20 then calculated to be 36.14942817=20 kcal/mole, quite a positive value. Similarly, we also obtained = a positive value of 2.77 = kcal/mol as the=20 van der waals energy between HD2 atom of TYR_178 in A chain and NE atom of = ARG_5001 in chain C.=20 We=20 are not sure about either our calculation is incorrect or it is = reasonable to=20 have positive van der waals=20 energy in those cases.

2.           = ;      =20 In the 1995 paper = by Cornell=20 et al., the scale factor of 1/2.0 is recommended for reducing the 1-4 = VDW=20 interactions as used previously by Weiner et al. (lines 6 to 8 from the = bottom=20 of the right-hand column in page 5183). Is our interpretation=20 correct?

 

Tabled Values for = TYR_178_A(HD2)(HA)-ARG_5001_C(CZ)(CA):

Ri*=3D 1.459

Rj*=3D1.908

Rij*=3D 3.367

=A3`i =3D 0.015

=A3`j =3D = 0.086

=A3`ij=3D(=A3`i=A3`j)^0.5=3D 0.035917

Aij=3D=A3`ij(Rij*)^12=3D 76245.16

Bij=3D2=A3`ij(Rij*)^6=3D 104.6607

Rij=3D 1.88247

Evdw=3DAij/(Rij^12)-Bij/(Rij^6)=3D = 36.14942817

 

We are looking forward to hearing from = you. Your=20 help in this respect is highly appreciated.

 

Sincerely Yours,

Yu-hui Fang

e-mail: p9894105{}ccmail.ncku.edu.tw

 

 

------=_NextPart_000_0013_01C7ADC9.A3E82400-- From owner-chemistry@ccl.net Wed Jun 13 11:13:00 2007 From: "Shobe, David David.Shobe....sud-chemie.com" To: CCL Subject: CCL:G: Limitations of DFT Message-Id: <-34473-070613104914-28235-ZZUaOR/37qPlcRLMojZ5sg..server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 13 Jun 2007 16:48:43 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe+/-sud-chemie.com] The real problem with DFT is as follows. The spin-restricted DFT (RDFT, as in Wai-To's response) FORCES pairing of every electron! If you have a diradical, RDFT will force the two unpaired electrons into the same orbital, which may or may not resemble either of the singly occupied orbitals in the diradical. And you may be using RDFT without being aware of it, because quantum-chemical programs in general use RDFT for any singlet species, unless you specify that UDFT (spin-unrestricted DFT) is to be used. Several months ago on CCL, there was a discussion on DFT (B3LYP?) calculations on the twisting of ethylene, and it may be helpful to review that discussion. The 90° twisted ethylene is very poorly described by DFT, because the two electrons are forced into one of the orthogonal p orbitals. Explicitly correlated methods such as CCSD or MP2 may be less vulnerable to this effect, because even though they rely on a single-determinant reference, they at least add in other determinants. Ideally one would use a multi-determinant reference method for problems like this, but they are not easy to use! --David Shobe -----Original Message----- > From: owner-chemistry+/-ccl.net [mailto:owner-chemistry+/-ccl.net] Sent: Wednesday, June 13, 2007 7:45 AM To: Shobe, David Subject: CCL:G: Limitations of DFT Sent to CCL by: Wai-To Chan [chan++curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< However, one of the reviewers on *this* manuscript objected to the use of the DFT calculations with the following: "With regards to using DFT calculations to distinguish between mechanisms B and C, I would put no confidence in such a result. It is well known that DFT calculations greatly overemphasize the stabilization provided by delocalization, so they have a built-in bias towards concerted reactions, which is useful if the reaction actually is concerted, but a disaster if it is not." Is this a true statement? And, if so, where can I find more about this limitation of DFT theory? I have searched but come up empty so far. Plus, I'm not sure exactly what the reviewer means, since the diradical intermediate of mechanism C would also be subject to delocalization effects...possibly even greater than those expected by a "concerted" reaction! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I assume reaction pathway (B) proceeds via a TS characterized by spin-restricted (R)DFT, (C) a open-shell TS characterized by unrestricted DFT and the reactant is closed-shell and treated by RDFT. Did you check the wavefunction stability of the TS for (B)? Instability of RHF and/or RDFT is a telling sign of discontinuity within your PES. The theoretical foundation underlying the characterization of the kind of PES with stationary points of varying degree of diradical character using single-reference type of methods is shaky. I however don't see any relevance of your reviewer's remarks to the limiation of DFT. DFT indeed does suffer from wavefunction stability and its reliability for the prediction of concerted and stepwise mechanism involving diradicals is seldom addressed. But I never heard of any studies which demonstrate that DFT is biased towards the concerted pathway. I seem to remember that DFT has been applied to characterization of the aromaticity of transition state structures in concerted reaction mechanism through NICS calculations. I am not familiar with the literature in this area but I doubt very much one can draw any conclusion from such studies alone on DFT's favouring of the concerted mehanism in pericyclic reactions. If I were you I would demand the referee to provide a reference to back up his/her comments further. Chance is that the referee's comments are merely speculations rather than established facts. It is not just DFT. The entire specturm of commonly employed single-reference type of methods (HF, MPn, CCSD(T), DFT) is inherently problematic for a consistently accurate characterization of a diradical PES. CASSCF in principle could solve the problem arising > from PES discontinuity. In practice CASSCF won't necessarily give more accurate structural and energetic predictions than DFT. DFT has been applied to the study of concerted and stepwise mechansims in cycloaddition reaction for years. Occassionaly serious discrepancies between DFT and CASSCF were noted. But no one to my knowledge has suggested DFT should be avoided in favour of other methods in general. There are other promising alternatives to DFT for diradical PES outside GAUSSIAN. Unless these methods have already gained general acceptance and are applicable to the system you are studying you don't have the obligation to 'upgrade' your DFT calculations in my view. My advice for you is to come up with a cogent response to the questions of the referee. You should in your discussion of your results highlight those limitations of the theories employed and convince the readers that the computations were properly executed within the limitations. As long as you lay out the facts clearly to allow the readers to assess your results you should stand a reasonable chance of getting your work accepted. Wai-To Chanhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Wed Jun 13 12:26:00 2007 From: "Pankaj R. Daga pdaga*_*olemiss.edu" To: CCL Subject: CCL: ONIOM Message-Id: <-34474-070613115652-20879-igGd6+3RXHYoRQDKAV8Pvg+/-server.ccl.net> X-Original-From: "Pankaj R. Daga" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0011_01C7ADA2.B18ACF80" Date: Wed, 13 Jun 2007 10:07:47 -0500 MIME-Version: 1.0 Sent to CCL by: "Pankaj R. Daga" [pdaga/./olemiss.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0011_01C7ADA2.B18ACF80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi everybody, I am new learner of ONIOM. I am dealing with a system with more than = 1000 atoms in it. I have divided the whole system into 3 layers. When I = am running the calculation with B3LYP/6-31G*:PM3:AM1, the calculations = run well. But when I use the same system with force field, amber or uff, = then program ends abruptly saying=20 "MM function not complete" I don't know if there is any need to add force-field parameters and if = yes then how? I see, there are a lot of reports available in the = literature using Amber force field in ONIOM method. I will be grateful to you if you could suggest me the way out. Thanx and Regards Pankaj =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D If your ship doesn't come in, swim out to it.......Jonathan Winters =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Pankaj R. Daga | =20 Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638 University of Mississippi | phone: +1-662-915-1853 University, MS, 38677-1848 | =20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_0011_01C7ADA2.B18ACF80 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi everybody,
 
I am new learner of ONIOM. I am = dealing=20 with a system with more than 1000 atoms in it. I have divided the whole = system=20 into 3 layers. When I am running the calculation with =20 B3LYP/6-31G*:PM3:AM1, the calculations run well. But when I use the same = system=20 with force field, amber or uff, then program ends abruptly saying =
 
"MM function not = complete"
I don't know if there is any = need to add=20 force-field parameters and if yes then how? I see, there are a lot of = reports=20 available in the literature using Amber force field in ONIOM=20 method.
 
I will be grateful to you if = you could=20 suggest me the way out.
 
Thanx and Regards
 
Pankaj
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
If=20 your ship doesn't come in, swim out to it.......Jonathan=20 Winters
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Pankaj= =20 R.=20 Daga           &nb= sp;        =20 | 
Department of Medicinal Chemistry  |  = e-mail: =20 pdaga_at_olemiss.edu
417 Faser Hall, School of Pharmacy | =20 fax:         =20 +1-662-915-5638
University of=20 Mississippi          = | =20 phone:        = +1-662-915-1853
University,=20 MS, 38677-1848         | =20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
------=_NextPart_000_0011_01C7ADA2.B18ACF80-- From owner-chemistry@ccl.net Wed Jun 13 13:06:00 2007 From: "Benjamin Ellingson ben++eyesopen.com" To: CCL Subject: CCL: Limitations of DFT Message-Id: <-34475-070613125146-10108-B3Uk0F94odfmehEVJdXY9g]![server.ccl.net> X-Original-From: "Benjamin Ellingson" Date: Wed, 13 Jun 2007 12:51:43 -0400 Sent to CCL by: "Benjamin Ellingson" [ben*|*eyesopen.com] >>>>>>>>>>>>>>>>>>>>>>>>>> The experimental results were not conclusive in differentiating beteen the mechanisms, so I proposed in the manuscript that a purely computationally-based follow-up paper on the intermediates, transition states (with IRC calculations), etc. at the DFT B3LYP/6-311+G(d,p) level of theory(a paper I am currently working on) would help to distiguish between the mechanisms. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< The single-reference and spin-restricted warnings already discussed are important points. Another thing to keep in mind is that the B3LYP method just isn't very good for kinetics. There are much better DFT methods for calculating transition states and minimum energy paths. All due respect to the immortal B3LYP, as it still holds its own when calculating atomization energies, but it is very difficult to do everything well. I would recommend using MPW1K and perhaps a newer method as well. A good paper to look at is "The Design of Density Functionals that are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions," Y. Zhao and D. G.. Truhlar, Journal of Physical Chemistry A 109, 5656-5667 (2005). There are newer functionals that are able to beat MPW1K in database MUE tests, but the older MPW1K just keeps sticking around towards the top and has build a track record. Like any functional, MPW1K sometimes gives bad results, but it appears that this is often caused by multi-reference issues, and not necessarily by a problem the functional itself. Ben Ellingson, Ph.D. Truhlar Group alum (<-disclosure) From owner-chemistry@ccl.net Wed Jun 13 13:44:01 2007 From: "Pablo Denis pablod(_)fq.edu.uy" To: CCL Subject: CCL:G: Limitations of DFT Message-Id: <-34476-070613133336-2616-UZ1TQc86t5Y7AiMc9n8K8w===server.ccl.net> X-Original-From: "Pablo Denis" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 13 Jun 2007 13:45:52 -0300 MIME-Version: 1.0 Sent to CCL by: "Pablo Denis" [pablod .. fq.edu.uy] Maybe the following references may help you JACS118-6036 concerted and stpewise mechanisms for DA reaction fo butadiene and ethylene and more or less the same for the stones wales transformation in C60 JACS125-5572 DFT has been used in both cases and for diradicals TS (JACS articles!!!)... Good luck, Pablo ----- Original Message ----- > From: "Shobe, David David.Shobe.#.sud-chemie.com" To: "Denis, Pablo Andres " Sent: Wednesday, June 13, 2007 11:48 AM Subject: CCL:G: Limitations of DFT > > Sent to CCL by: "Shobe, David" [David.Shobe+/-sud-chemie.com] > The real problem with DFT is as follows. The spin-restricted DFT (RDFT, > as in Wai-To's response) FORCES pairing of every electron! If you have a > diradical, RDFT will force the two unpaired electrons into the same > orbital, which may or may not resemble either of the singly occupied > orbitals in the diradical. > > And you may be using RDFT without being aware of it, because > quantum-chemical programs in general use RDFT for any singlet species, > unless you specify that UDFT (spin-unrestricted DFT) is to be used. > > Several months ago on CCL, there was a discussion on DFT (B3LYP?) > calculations on the twisting of ethylene, and it may be helpful to review > that discussion. The 90° twisted ethylene is very poorly described by > DFT, because the two electrons are forced into one of the orthogonal p > orbitals. > > Explicitly correlated methods such as CCSD or MP2 may be less vulnerable > to this effect, because even though they rely on a single-determinant > reference, they at least add in other determinants. > > Ideally one would use a multi-determinant reference method for problems > like this, but they are not easy to use! > > --David Shobe > > -----Original Message----- >> From: owner-chemistry]*[ccl.net [mailto:owner-chemistry]*[ccl.net] > Sent: Wednesday, June 13, 2007 7:45 AM > To: Shobe, David > Subject: CCL:G: Limitations of DFT > > > Sent to CCL by: Wai-To Chan [chan++curl.gkcl.yorku.ca] > > > <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< > However, one of the reviewers on *this* manuscript > objected to the use of the DFT calculations with the following: > "With regards to using DFT calculations to distinguish between mechanisms > B > and C, I would put no confidence in such a result. It is well known that > DFT > calculations greatly overemphasize the stabilization provided by > delocalization, > so they have a built-in bias towards concerted reactions, which is useful > if the > reaction actually is concerted, but a disaster if it is not." > Is this a true statement? And, if so, where can I find more about this > limitation of DFT theory? I have searched but come up empty so far. Plus, > I'm > not sure exactly what the reviewer means, since the diradical intermediate > of > mechanism C would also be subject to delocalization effects...possibly > even > greater than those expected by a "concerted" reaction! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > > I assume reaction pathway (B) proceeds via a TS characterized > by spin-restricted (R)DFT, (C) a open-shell TS characterized by > unrestricted DFT and the reactant is closed-shell and treated by RDFT. > Did you check the wavefunction stability of the TS for (B)? Instability of > RHF and/or RDFT > is a telling sign of discontinuity within your PES. > > The theoretical foundation underlying the characterization of the kind of > PES > with stationary points of varying degree of diradical character > using single-reference type of methods is shaky. I however don't see any > relevance of your > reviewer's remarks to the limiation of DFT. DFT indeed does suffer from > wavefunction stability and > its reliability for the prediction of concerted and stepwise mechanism > involving > diradicals is seldom addressed. But I never heard of any studies which > demonstrate > that DFT is biased towards the concerted pathway. I seem to > remember that DFT has been applied to characterization of the aromaticity > of transition > state structures in concerted reaction mechanism through NICS > calculations. > I am not familiar with the literature in this area but I doubt very much > one can draw any conclusion from such studies alone on DFT's favouring > of the concerted mehanism in pericyclic reactions. > If I were you I would demand the referee to provide > a reference to back up his/her comments further. Chance is that the > referee's > comments are merely speculations rather than established facts. > > It is not just DFT. The entire specturm of commonly employed > single-reference type of methods (HF, MPn, CCSD(T), DFT) > is inherently problematic for a consistently accurate characterization > of a diradical PES. CASSCF in principle could solve the problem arising >> from PES discontinuity. In practice CASSCF won't necessarily give more >> accurate structural > and energetic predictions than DFT. > DFT has been applied to the study of concerted and stepwise mechansims > in cycloaddition reaction for years. Occassionaly serious discrepancies > between > DFT and CASSCF were noted. But no one to my knowledge has suggested > DFT should be avoided in favour of other methods in general. There are > other > promising alternatives to DFT for diradical PES outside GAUSSIAN. > Unless these methods have already gained general acceptance and are > applicable to the > system you are studying you don't have the obligation to 'upgrade' > your DFT calculations in my view. My advice for you is > to come up with a cogent response to the questions of the referee. You > should > in your discussion of your results highlight those limitations of the > theories employed and convince the readers that the computations were > properly executed within the limitations. As long as you lay out the facts > clearly to allow the > readers to assess your results you should stand a reasonable chance of > getting your work accepted. > > Wai-To > Chanhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis > e-mail message may contain confidential and / or privileged information. > If you are not an addressee or otherwise authorized to receive this > message, you should not use, copy, disclose or take any action based on > this e-mail or any information contained in the message. If you have > received this material in error, please advise the sender immediately by > reply e-mail and delete this message. > Thank you.> > > > > -- > No virus found in this incoming message. > Checked by AVG Free Edition. > Version: 7.5.472 / Virus Database: 269.8.15/847 - Release Date: 12/06/2007 > 09:42 p.m. > From owner-chemistry@ccl.net Wed Jun 13 14:56:00 2007 From: "Marius Retegan marius.s.retegan=gmail.com" To: CCL Subject: CCL:G: ONIOM Message-Id: <-34477-070613143430-11671-NXiF5WPR9HXwNjj9BqvbrQ()server.ccl.net> X-Original-From: "Marius Retegan" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 13 Jun 2007 20:27:18 +0200 MIME-Version: 1.0 Sent to CCL by: "Marius Retegan" [marius.s.retegan]![gmail.com] Hi, First of all I would like to say that I don't see the sens on using a three layer ONIOM in which two of the layers are calculated with PM3 and AM1. These to methods provide similar results and I think that it would be logical to use a 2 layer ONIOM (b3lyp/pm3 or b3lyp/am1). About the error, I can't give you an explanation since I don't know how you did make your input. I find that doing ONIOM inputs for Gaussian can be hard to very hard if you don't have GaussView, and even if you have can still be tricky the first time you try it. Another tool that you can use to create inputs ( in the case that you don't have GV) is Gabedit. A new version of Gabedit (2.0.11) is available. Here is a list of the significant changes between 2.0.11 and 2.0.7: - Bugs were fixed. - PCGamess is now supported by Gabedit - Q-Chem is now supported by Gabedit - New windows for draw IR, Raman and UV/Visible spectrum. - The ONIOM method of Gaussian is now supported You can download this new version from : http://lasim.univ-lyon1.fr/allouche/gabedit/download.php Hope this helps Marius Retegan On 6/13/07, Pankaj R. Daga pdaga*_*olemiss.edu wrote: > > > Hi everybody, > > I am new learner of ONIOM. I am dealing with a system with more than 1000 > atoms in it. I have divided the whole system into 3 layers. When I am > running the calculation with B3LYP/6-31G*:PM3:AM1, the calculations run > well. But when I use the same system with force field, amber or uff, then > program ends abruptly saying > > "MM function not complete" > > I don't know if there is any need to add force-field parameters and if yes > then how? I see, there are a lot of reports available in the literature > using Amber force field in ONIOM method. > > I will be grateful to you if you could suggest me the way out. > > Thanx and Regards > > Pankaj > > =================================================================== > If your ship doesn't come in, swim out to it.......Jonathan Winters > =================================================================== > Pankaj R. Daga | > Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu > 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638 > University of Mississippi | phone: +1-662-915-1853 > University, MS, 38677-1848 | > =================================================================== From owner-chemistry@ccl.net Wed Jun 13 16:13:00 2007 From: "Pankaj R. Daga pdaga(-)olemiss.edu" To: CCL Subject: CCL:G: ONIOM Message-Id: <-34478-070613160602-12578-tzrnmJSEzRnRMJhx/8BwIA]~[server.ccl.net> X-Original-From: "Pankaj R. Daga" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0004_01C7ADCC.568F3D30" Date: Wed, 13 Jun 2007 15:05:54 -0500 MIME-Version: 1.0 Sent to CCL by: "Pankaj R. Daga" [pdaga : olemiss.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0004_01C7ADCC.568F3D30 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Marius=20 Thanx for your inputs. Actually, I should have mentioned it in my previous mail itself. I have = used GV to generate the output file. Secondmost, I agree there is no sense in using 3-layer ONIOM in which 2 = layers being treated with semi-empirical level. In the very beginning, I = faced error in DFT:PM3:Amber method. So I just wanted to know if the = problem is with my input file or with the Gaussian. So to check if input = file is fine, I tried the second example with DFT:PM3:AM1. It worked = fine. So, it seems my input file is fine.=20 Could you please now help me to solve, how we can deal with force-field = related problem? I would be grateful to you Pankaj =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D If your ship doesn't come in, swim out to it.......Jonathan Winters =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Pankaj R. Daga | =20 Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638 University of Mississippi | phone: +1-662-915-1853 University, MS, 38677-1848 | =20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ----- Original Message -----=20 > From: "Marius Retegan marius.s.retegan=3Dgmail.com" = To: "Daga, Pankaj R " Sent: Wednesday, June 13, 2007 1:27 PM Subject: CCL:G: ONIOM >=20 > Sent to CCL by: "Marius Retegan" [marius.s.retegan]![gmail.com] > Hi, > First of all I would like to say that I don't see the sens on using a > three layer ONIOM in which two of the layers are calculated with PM3 > and AM1. These to methods provide similar > results and I think that it would be logical to use a 2 layer ONIOM > (b3lyp/pm3 or b3lyp/am1). >=20 > About the error, I can't give you an explanation since I don't know > how you did make your input. I find that doing ONIOM inputs for > Gaussian can be hard to very hard if you don't have GaussView, and > even if you have can still be tricky the first time you try it. > Another tool that you can use to create inputs ( in the case that you > don't have GV) is Gabedit. >=20 > A new version of Gabedit (2.0.11) is available. >=20 > Here is a list of the significant changes between 2.0.11 and 2.0.7: > - Bugs were fixed. > - PCGamess is now supported by Gabedit > - Q-Chem is now supported by Gabedit > - New windows for draw IR, Raman and UV/Visible spectrum. > - The ONIOM method of Gaussian is now supported >=20 > You can download this new version from : > http://lasim.univ-lyon1.fr/allouche/gabedit/download.php >=20 > Hope this helps > Marius Retegan >=20 >=20 >=20 > On 6/13/07, Pankaj R. Daga pdaga*_*olemiss.edu = wrote: >> >> >> Hi everybody, >> >> I am new learner of ONIOM. I am dealing with a system with more than = 1000 >> atoms in it. I have divided the whole system into 3 layers. When I am >> running the calculation with B3LYP/6-31G*:PM3:AM1, the calculations = run >> well. But when I use the same system with force field, amber or uff, = then >> program ends abruptly saying >> >> "MM function not complete" >> >> I don't know if there is any need to add force-field parameters and = if yes >> then how? I see, there are a lot of reports available in the = literature >> using Amber force field in ONIOM method. >> >> I will be grateful to you if you could suggest me the way out. >> >> Thanx and Regards >> >> Pankaj >> >> = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D >> If your ship doesn't come in, swim out to it.......Jonathan Winters >> = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D >> Pankaj R. Daga | >> Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu >> 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638 >> University of Mississippi | phone: +1-662-915-1853 >> University, MS, 38677-1848 | >> = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D >=20 >=20 >=20 > -=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>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search) >=20>=20>=20 > =>=20 >=20 >=20 > ------=_NextPart_000_0004_01C7ADCC.568F3D30 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear=20 Marius
 
Thanx for your = inputs.
 
Actually, I should have = mentioned it in my=20 previous mail itself. I have used GV to generate the output = file.
 
Secondmost, I agree there is no = sense in=20 using 3-layer ONIOM in which 2 layers being treated with semi-empirical = level.=20 In the very beginning, I faced error in DFT:PM3:Amber method. So I just = wanted=20 to know if the problem is with my input file or with the Gaussian. So to = check=20 if input file is fine, I tried the second example with DFT:PM3:AM1. It = worked=20 fine. So, it seems my input file is fine.
 
Could you please now help me to = solve, how=20 we can deal with force-field related problem?
 
I would be grateful to = you
 
Pankaj
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
If=20 your ship doesn't come in, swim out to it.......Jonathan=20 Winters
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Pankaj= =20 R.=20 Daga           &nb= sp;        =20 | 
Department of Medicinal Chemistry  |  = e-mail: =20 pdaga_at_olemiss.edu
417 Faser Hall, School of Pharmacy | =20 fax:         =20 +1-662-915-5638
University of=20 Mississippi          = | =20 phone:        = +1-662-915-1853
University,=20 MS, 38677-1848         | =20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 
 
----- Original Message ----- =
From: "Marius Retegan=20 marius.s.retegan=3Dgmail.com" <owner-chemistry * ccl.net>
To: "Daga, Pankaj R " = <pdaga * olemiss.edu>
Sent: Wednesday, June 13, 2007 = 1:27=20 PM
Subject: CCL:G: = ONIOM

>
> Sent to CCL by: "Marius = Retegan"=20 [marius.s.retegan]![gmail.com]
> Hi,
> First of all I would = like to=20 say that I don't see the sens on using a
> three layer ONIOM in = which two=20 of the layers are calculated with PM3
> and AM1. These to methods = provide=20 similar
> results and I think that it would be logical to use a 2 = layer=20 ONIOM
> (b3lyp/pm3 or b3lyp/am1).
>
> About the = error, I=20 can't give you an explanation since I don't know
> how you did = make your=20 input. I find that doing ONIOM inputs for
> Gaussian can be hard = to very=20 hard if you don't have GaussView, and
> even if you have can still = be=20 tricky the first time you try it.
> Another tool that  you = can use to=20 create inputs ( in the case that you
> don't have GV) is = Gabedit.
>=20
> A new version of Gabedit (2.0.11) is available.
> =
> Here=20 is a list of the significant changes between 2.0.11 and 2.0.7:
> - = Bugs=20 were fixed.
> - PCGamess is now supported by Gabedit
> - = Q-Chem is=20 now supported by Gabedit
> - New windows for draw IR, Raman and = UV/Visible=20 spectrum.
> - The ONIOM method of Gaussian is now = supported
>=20
> You can download this new version from :
> http://lasim.univ-lyon1.fr/allouche/gabedit/download.php<= /A>
>
> Hope this helps
> = Marius=20 Retegan
>
>
>
> On 6/13/07, Pankaj R. Daga=20 pdaga*_*olemiss.edu <owner-chemistry],[ccl.net>=20 wrote:
>>
>>
>> Hi = everybody,
>>
>>=20 I am new learner of ONIOM. I am dealing with a system with more than=20 1000
>> atoms in it. I have divided the whole system into 3 = layers.=20 When I am
>> running the calculation with  = B3LYP/6-31G*:PM3:AM1,=20 the calculations run
>> well. But when I use the same system = with force=20 field, amber or uff, then
>> program ends abruptly=20 saying
>>
>> "MM function not=20 complete"
>>
>> I don't know if there is any need to = add=20 force-field parameters and if yes
>> then how? I see, there are = a lot=20 of reports available in the literature
>> using Amber force = field in=20 ONIOM method.
>>
>> I will be grateful to you if you = could=20 suggest me the way out.
>>
>> Thanx and=20 Regards
>>
>> Pankaj
>>
>>=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>>=20 If your ship doesn't come in, swim out to it.......Jonathan = Winters
>>=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>>=20 Pankaj R.=20 Daga           &nb= sp;        =20 |
>> Department of Medicinal Chemistry  |  = e-mail: =20 pdaga_at_olemiss.edu
>> 417 Faser Hall, School of Pharmacy = | =20 fax:         =20 +1-662-915-5638
>> University of=20 Mississippi          = | =20 phone:        = +1-662-915-1853
>>=20 University, MS, = 38677-1848        =20 |
>>=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
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> ------=_NextPart_000_0004_01C7ADCC.568F3D30-- From owner-chemistry@ccl.net Wed Jun 13 17:36:00 2007 From: "Chad Risko risko^_^northwestern.edu" To: CCL Subject: CCL: ORCA and ECP basis sets Message-Id: <-34479-070613083311-31455-P/1t6ITFX5s2wxuCNkbUoQ:server.ccl.net> X-Original-From: "Chad Risko" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 13 Jun 2007 06:41:10 -0500 MIME-Version: 1.0 Sent to CCL by: "Chad Risko" [risko[A]northwestern.edu] Frank - Thank you for the response. I look forward to seeing the new version of ORCA soon. Regards, Chad -----Original Message----- > From: owner-chemistry*o*ccl.net [mailto:owner-chemistry*o*ccl.net] Sent: Wednesday, June 13, 2007 2:58 AM To: Risko, Chad Subject: CCL: ORCA and ECP basis sets Sent to CCL by: Frank Neese [neese-,-thch.uni-bonn.de] Dear Chad, unfortunately, ECP's are not yet available in ORCA. Since we have realized that this is a serious shortcoming, we are presently working on it and there is some hope that it becomes available in the late summer or autmun. At this point, geometry optimizations for gold containing clusters are only possible with a scalar relativistic all electron approach which is, of course, much more expensive than the ECP calculations. Once the ECP's become available in ORCA we will likely follow the GAMESS US format in EMSL since we have all other basis input in this format. The problems with the mailing list are acknowledged and should be corrected in the near future. With my best regards, Frank Neesehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt