From owner-chemistry@ccl.net Tue Feb 6 01:34:00 2007 From: "Ben Vastine vastinator-*-gmail.com" To: CCL Subject: CCL:G: running the new 2-PLYP density functional in Gaussian03 Message-Id: <-33534-070206012458-7780-ZkaVtlIUU8mG8nThDa7NDQ]![server.ccl.net> X-Original-From: "Ben Vastine" Content-Type: multipart/alternative; boundary="----=_Part_97_19962469.1170741462008" Date: Mon, 5 Feb 2007 23:57:42 -0600 MIME-Version: 1.0 Sent to CCL by: "Ben Vastine" [vastinator]^[gmail.com] ------=_Part_97_19962469.1170741462008 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline All: I would like to run the new 2-PLYP density functionals of Grimme et al., but I've been unable to get them to run. In one of their papers, the authors state that the mPW2-PLYP density functional will run with this route card entry: # mpwlyp/cc-pvtz iop(3/76=0450005500,3/78=0750007500) extraoverlay scf=tight 8/10=90/1;9/16=-3/6 I typed that into my Gaussian input file, and got this error message: %chk=/home/usr/1.chk %mem=500mb %nproc=1 Will use up to 2 processors via shared memory. ---------------------------------------------------------------------- #p mpwlyp/cc-pvdz iop(3/76=0450005500,3/78=0750007500) extraoverlay 8/ 10=90/1;9/16=-3/6 ---------------------------------------------------------------------- QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. 78=0750007500) EXTRAOVERLAY 8/10=90/1;9/ Gaussian did not like the 8/10... part of the input file. What am I doing wrong? Thanks Ben ref: Schwabe & Grimme Physical Chemistry Chemical Physics 2006, 8, 4398-4401. ' ------=_Part_97_19962469.1170741462008 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline All:

I would like to run the new 2-PLYP density functionals of Grimme et al., but I've been unable to get them to run. In one of their papers, the authors state that the mPW2-PLYP density functional will run with this route card entry:

# mpwlyp/cc-pvtz iop(3/76=0450005500,3/78=0750007500) extraoverlay scf=tight 8/10=90/1;9/16=-3/6

I typed that into my Gaussian input file, and got this error message:

%chk=/home/usr/1.chk
%mem=500mb
%nproc=1
Will use up to 2 processors via shared memory.
----------------------------------------------------------------------
#p mpwlyp/cc-pvdz iop(3/76=0450005500,3/78=0750007500) extraoverlay 8/
10=90/1;9/16=-3/6
----------------------------------------------------------------------
QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.
78=0750007500) EXTRAOVERLAY 8/10=90/1;9/

Gaussian did not like the 8/10... part of the input file.

What am I doing wrong?

Thanks

Ben

ref: Schwabe & Grimme Physical Chemistry Chemical Physics 2006, 8, 4398-4401.
'

------=_Part_97_19962469.1170741462008-- From owner-chemistry@ccl.net Tue Feb 6 03:08:00 2007 From: "Sangeetha Subramaniam srdshigella() gmail.com" To: CCL Subject: CCL: Visualization Freeware Message-Id: <-33535-070205075759-19394-SaXQK9oBFaGKLgdDdewT3A:_:server.ccl.net> X-Original-From: "Sangeetha Subramaniam" Content-Type: multipart/alternative; boundary="----=_Part_16261_4967089.1170678505915" Date: Mon, 5 Feb 2007 16:58:25 +0430 MIME-Version: 1.0 Sent to CCL by: "Sangeetha Subramaniam" [srdshigella---gmail.com] ------=_Part_16261_4967089.1170678505915 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Young Leh, PyMol is good for your purpose. Also have a look a molmol .. both produce very good images.. sangeetha. Mrs.S.Sangeetha Research Assistant C/O Dr.Dinesh Gupta, Structural & Computational Biology Group Internationa centre for Genetic Engineering and Biotechnology(ICGEB), Aruna Asaf Ali Marg NewDelhi-110067. On 2/5/07, Young Leh youngleh a gmail.com wrote: > > > Sent to CCL by: "Young Leh" [youngleh{=}gmail.com] > Dear CCLer, > > I am now looking for a visualization freeware that can be used to produce > 3D molecular pictures with publishable quality. Could somebody please give > me some hints? > > Thanks and have a great day. > > Young Leh> > > > -- S.Sangeetha Research Assistant, C/o Dr.Dinesh Gupta, Structural and Computational Biology, International Center for Genetic Engineering and Biotechnology, Aruna asaf ali marg, NewDelhi-110067 Mobile : +91 98910 64332 Web : http://www.icgeb.org ------=_Part_16261_4967089.1170678505915 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Young Leh,

PyMol is good for your purpose. Also have a look a molmol ..
both produce very good images..

sangeetha.

Mrs.S.Sangeetha
Research Assistant
C/O Dr.Dinesh Gupta,
Structural & Computational Biology Group
Internationa centre for Genetic Engineering 

and Biotechnology(ICGEB),
Aruna Asaf Ali Marg
NewDelhi-110067.

On 2/5/07, Young Leh youngleh a gmail.com <owner-chemistry^^^ccl.net> wrote:

Sent to CCL by: "Young  Leh" [youngleh{=}gmail.com]
Dear CCLer,

I am now looking for a visualization freeware that can be used to produce 3D molecular pictures with publishable quality.  Could somebody please give me some hints?

Thanks and have a great day.

Young Leh

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--
S.Sangeetha
Research Assistant,
C/o Dr.Dinesh Gupta,
Structural and Computational Biology,
International Center for Genetic Engineering and Biotechnology,
Aruna asaf ali marg,
NewDelhi-110067

Mobile : +91 98910 64332
Web : http://www.icgeb.org ------=_Part_16261_4967089.1170678505915-- From owner-chemistry@ccl.net Tue Feb 6 03:42:01 2007 From: "Miklos Vargyas miklos.vargyas : chemaxon.hu" To: CCL Subject: CCL: Visualization Freeware Message-Id: <-33536-070205063232-11766-EwKUjciZ8L/gQzITxJLHxA|*|server.ccl.net> X-Original-From: Miklos Vargyas Content-Type: multipart/alternative; boundary="------------070806080002080403000209" Date: Mon, 05 Feb 2007 11:36:34 +0100 MIME-Version: 1.0 Sent to CCL by: Miklos Vargyas [miklos.vargyas*|*chemaxon.hu] This is a multi-part message in MIME format. --------------070806080002080403000209 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Young Leh, try MarvinSpace! It can produce high quality 3D images, and it does support arbitrary custom resolution and save images in common graphical file formats (like PNG, JPG etc). You may wish to visit the MarvinSpace image gallery to get an impression about the rendering quality of the software: http://www.chemaxon.com/marvinspace/gallery.html Our software tools are free for academic users and non-commercial web sites. Follow this link if you would like to subscribe for the free usage or need more details: http://www.chemaxon.com/licensing.html The MarvinSpace application is also free if it is not used as integral part of other applications - which, as I understand, is your case. The MarvinSpace application (http://www.chemaxon.com/marvin/doc/user/mspace.html) is available in the Marvin Beans package that can be dowloaded at the Marvin site (locate the Download link at http://www.chemaxon.com/marvin/ ). Regards, Miklos Vargyas Young Leh youngleh a gmail.com wrote: >Sent to CCL by: "Young Leh" [youngleh{=}gmail.com] >Dear CCLer, > >I am now looking for a visualization freeware that can be used to produce 3D molecular pictures with publishable quality. Could somebody please give me some hints? > >Thanks and have a great day. > >Young Leh> > > > > > --------------070806080002080403000209 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Young Leh,

try MarvinSpace! It can produce high quality 3D images, and it does support arbitrary custom resolution and save images in common graphical file formats (like PNG, JPG etc).

You may wish to visit the MarvinSpace image gallery to get an impression about the rendering quality of the software:
http://www.chemaxon.com/marvinspace/gallery.html

Our software tools are free for academic users and non-commercial web sites. Follow this link if you would like to subscribe for the free usage or need more details: http://www.chemaxon.com/licensing.html

The MarvinSpace application is also free if it is not used as integral part of other applications - which, as I understand, is your case.

The MarvinSpace application (http://www.chemaxon.com/marvin/doc/user/mspace.html) is available in the Marvin Beans package that can be dowloaded at the Marvin site (locate the Download link at http://www.chemaxon.com/marvin/).

Regards,
Miklos Vargyas

Young Leh youngleh a gmail.com wrote:

Sent to CCL by: "Young  Leh" [youngleh{=}gmail.com]
Dear CCLer,

I am now looking for a visualization freeware that can be used to produce 3D molecular pictures with publishable quality.  Could somebody please give me some hints?

Thanks and have a great day.

Young LehE-mail to subscribers: CHEMISTRY]^[ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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We are testing and comparing outputs obtained from Jaguar an= d Gaussian03 suites. We have determined that the geometries obtained b= y optimizing with either program are almost identical. However, the en= ergies differ significantly.

The things we have done so far to try to narrow down the reason for the dis= crepancies in the energies are:
1)       Compar= ed different methods (i.e., HF vs B3LYP) and regardless of the method the en= ergy difference remains suggesting that the error is not dependent on DFT or= ab initio methods
2)       Compar= ed basis sets (i.e., 6-31G(d), 6-311+G(3df,3pd)) although Jaguar uses pseudo= spectral method on the smaller basis set it uses analytic for the larger bas= is set. Suggesting that the error is not dependent on either analytic = or pseudospectral methods.
3)       Compar= ed the definition of the basis sets (i.e., comparing basis set libraries) an= d these are identical between Jaguar and Gaussian
4)       Compar= ed using 6D and 5D orbitals and still the difference remains.

Any assistance in determining the source of the difference in energies woul= d be greatly appreaciated.

Ken Hunter

--
T. Daniel Crawford &n= bsp; = Department of Chemistry
crawdad#,#vt.edu = &nbs= p; Vi= rginia Tech
www.chem.vt.edu/faculty/crawford.php Voice: 540-231-7760 FAX: 5= 40-231-3255
 &nb= sp; &= nbsp; --------------------
PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt<= BR> --B_3253606500_60916707-- From owner-chemistry@ccl.net Tue Feb 6 12:43:00 2007 From: "Manuel Piacenza mpiacenza]![web.de" To: CCL Subject: CCL:G: running the new 2-PLYP density functional in Gaussian03 Message-Id: <-33543-070206051621-15752-KHIFoPfBwp2c13Y7XL4TnA]=[server.ccl.net> X-Original-From: Manuel Piacenza Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 6 Feb 2007 10:22:21 +0100 MIME-Version: 1.0 Sent to CCL by: Manuel Piacenza [mpiacenza*o*web.de] There must be an additional semicolon at the end of the input line: extraoverlay 8/10=90/1;9/16=-3/6; This should be working with Gaussian03. Regards Manuel Am Dienstag 06 Februar 2007 06:57 schrieb Ben Vastine vastinator-*-gmail.com: > All: > > I would like to run the new 2-PLYP density functionals of Grimme et al., > but I've been unable to get them to run. In one of their papers, the > authors state that the mPW2-PLYP density functional will run with this > route card entry: > > # mpwlyp/cc-pvtz iop(3/76=0450005500,3/78=0750007500) extraoverlay > scf=tight 8/10=90/1;9/16=-3/6 > > I typed that into my Gaussian input file, and got this error message: > > > %chk=/home/usr/1.chk > %mem=500mb > %nproc=1 > Will use up to 2 processors via shared memory. > ---------------------------------------------------------------------- > #p mpwlyp/cc-pvdz iop(3/76=0450005500,3/78=0750007500) extraoverlay 8/ > 10=90/1;9/16=-3/6 > ---------------------------------------------------------------------- > QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. > 78=0750007500) EXTRAOVERLAY 8/10=90/1;9/ > > > Gaussian did not like the 8/10... part of the input file. > > What am I doing wrong? > > Thanks > > Ben > > ref: Schwabe & Grimme Physical Chemistry Chemical Physics 2006, 8, > 4398-4401. > ' From owner-chemistry@ccl.net Tue Feb 6 14:44:00 2007 From: "Mark Thompson mark[#]arguslab.com" To: CCL Subject: CCL: Visualization Freeware Message-Id: <-33544-070206131500-31959-SoR0Y54P1oRXGVeU6GOPBQ[]server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 06 Feb 2007 09:27:02 -0800 MIME-Version: 1.0 Sent to CCL by: Mark Thompson [mark^^^arguslab.com] ArgusLab (www.arguslab.com) is free and exports jpeg and bitmap images (rendered in OpenGl) as well as files that can be rendered with PovRay Mark > > Young Leh youngleh a gmail.com wrote: >> Sent to CCL by: "Young Leh" [youngleh{=}gmail.com] >> Dear CCLer, >> >> I am now looking for a visualization freeware that can be used to produce 3D molecular pictures with publishable quality. Could somebody please give me some hints? >> >> Thanks and have a great day. >> >> Young LehE-mail to subscribers: CHEMISTRY[-]ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST[-]ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- ************************************ Mark Thompson Planaria Software LLC http://www.arguslab.com mark .. arguslab.com ************************************ From owner-chemistry@ccl.net Tue Feb 6 15:23:00 2007 From: "Adil Zhugralin zhugrali[a]bc.edu" To: CCL Subject: CCL:G: Thermodynamics and kinetics with DFT for organometallic systems Message-Id: <-33545-070206152139-31409-SU+6lBNVjf3kV3LVhn4Wkw(~)server.ccl.net> X-Original-From: "Adil Zhugralin" Date: Tue, 6 Feb 2007 15:21:35 -0500 Sent to CCL by: "Adil Zhugralin" [zhugrali~!~bc.edu] Dear CCL'ers: First of all thank you all for responding to my previous posting regarding the DF's for reaction pathway calculations in g03 for organometallic catalytic cycles. Well, I have a follow up question now. If I am going to use, say, MPW1K to calculate reaction barrier, but all my intermediates were calculated with, say, BP86, would these energies be flawed. My understanding is that the authors of MPW1K state that this DF is not good for energetics and geometries of stable molecules. Would I have to employ MPW1K separately from BP86 in my studies, but use BP86 for reactive intermediates and MPW1K for transition states? Would such a comparison be valid at all? I'm sorry if this is a naive question, which it is, but I am very new to this. Any answers would be greatly appreciated. Thank you very much in advance, Adil From owner-chemistry@ccl.net Tue Feb 6 16:22:00 2007 From: "Kalju Kahn kalju : chem.ucsb.edu" To: CCL Subject: CCL: Visualization Freeware Message-Id: <-33546-070205134149-3637-0UrvqLVww0Je50yNyrV84Q^-^server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 05 Feb 2007 04:52:30 -0800 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju^chem.ucsb.edu] Dear Young, Here are my favorites: PyMol (general, strength in biomolecules) http://pymol.sourceforge.net/ see http://www.chem.ucsb.edu/~molvisual/ for scripting examples Chimera (general, nice nucleic acids) http://www.cgl.ucsf.edu/chimera/ gOpenMol (if you have MD trajectories) http://www.csc.fi/gopenmol/ Molekel (lots of surface properties) http://www.cscs.ch/molekel/ Molden -> OpenGL export / moldenogl (small molecule QM electrostatic potentail maps) http://www.cmbi.ru.nl/molden/molden.html see http://www.chem.ucsb.edu/~kalju/chem162/public/task2A.html for a tutorial. Hope this helps, Kalju ------------------- > > Sent to CCL by: "Young Leh" [youngleh{=}gmail.com] > Dear CCLer, > > I am now looking for a visualization freeware that can be used to produce 3D molecular pictures with publishable quality. Could somebody please give me some hints? > > Thanks and have a great day. > > Young Leh> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -+ > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara From owner-chemistry@ccl.net Tue Feb 6 17:14:01 2007 From: "Wai-To Chan chan%a%curl.gkcl.yorku.ca" To: CCL Subject: CCL:G: Thermodynamics and kinetics with DFT for organometallic systems Message-Id: <-33547-070206171055-21809-fqYhtlRl75UgUodW6isi9w*_*server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 6 Feb 2007 17:29:58 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan * curl.gkcl.yorku.ca] Sorry to interject another question without answering yours. Is that MPW1K has been shown to be the choice of DFT method for reaction barriers for the kinetics of organometallic systems? I seem to remember MPW1K was calibrated against accurate barriers to mainly organic radical reactions when it was first reported. Did the Truhlar group recommend MPW1K for organometallic reactions as well in follow-up works? Could someone points to me references on the accuracy of the application of MPW1K to organometallic systems which I might have missed? Thanks. Wai-To Chan <<<<<<<<<<<<<<<< Dear CCL'ers: First of all thank you all for responding to my previous posting regarding the DF's for reaction pathway calculations in g03 for organometallic catalytic cycles. Well, I have a follow up question now. If I am going to use, say, MPW1K to calculate reaction barrier, but all my intermediates were calculated with, say, BP86, would these energies be flawed. My understanding is that the authors of MPW1K state that this DF is not good for energetics and geometries of stable molecules. Would I have to employ MPW1K separately from BP86 in my studies, but use BP86 for reactive intermediates and MPW1K for transition states? Would such a comparison be valid at all? I'm sorry if this is a naive question, which it is, but I am very new to this. Any answers would be greatly appreciated. Thank you very much in advance, Adil >>>>>>>>>>>> From owner-chemistry@ccl.net Tue Feb 6 18:24:01 2007 From: "Adil Zhugralin zhugrali||bc.edu" To: CCL Subject: CCL:G: summary about DFTs for organometallics Message-Id: <-33548-070206182248-21899-sklffzX+CsUY3mk7pEq+Qg###server.ccl.net> X-Original-From: "Adil Zhugralin" Date: Tue, 6 Feb 2007 18:22:45 -0500 Sent to CCL by: "Adil Zhugralin" [zhugrali(0)bc.edu] Dear all, I'm sorry I didn't post the summary of all the answers I got. Thanks to all who responded to my previous question here. As for MPW1K, I got a response suggesting it is good for kinetic barriers with organometallics (see below). I got an e-mail from Yan Zhao suggesting M06-L density functional. Here's a summary of all the answers I've got previously to the following question: ------------------------------ QUESTION: Dear all: I am trying to execute calculations on catalytic cycle involving ruthenium carbenes. I am experimentalist, but these calculations are essential for my research. Based on the little that I've read so far, DFT methods like B3LYP are generally not so good for organometallics. People in my field use either BP86 or PW91, but none of these are any good for calculating kinetic barriers. Recently Truhlar and co-workers disclosed a few new meta-hybrid-GGA's like M05 and M06, so I was wondering if anyone knows anything about them, that is to say, how reliable are they? Also, how would one go about obtaining them if necessary? And the last question: What basis sets would perform better for organometallics? (I'm trying to use 6-31G* on all atoms except Ru, for which I'm using Stuttgart/Dresden RECP). Thank you all! Adil ANSWERS: ----------------------------- Please don't forget the functionals containing optimized exchange (OPTX) like OPBE and OLYP; not only are they GGA's, thus much faster than hybrids, also they perform very well for spin states of organometallic systems, accuracy of geometries, as well as the energies and structures of transition states. In a recent study where we compared DFT with CCSD(T) calculations, the best performance was observed by mPBE0KCIS/QZ4P//OLYP/QZ4P. The same methodology has been used in a recent study on nucleophilic substitution at phosphorus. See for instance: M. Swart, A.W. Ehlers and K. Lammertsma "Performance of the OPBE exchange-correlation functional" Mol. Phys. 2004, 102, 2467-2474 M. Swart, A.R. Groenhof, A.W. Ehlers and K. Lammertsma "Validation of exchange-correlation functionals for spin states of iron-complexes" J. Phys. Chem. A 2004, 108, 5479-5483 M.A. van Bochove, M. Swart and F.M. Bickelhaupt "Nucleophilic substitution at phosphorus (SN2:+:P): Disappearance and reappearance of reaction barriers" J. Am. Chem. Soc. 2006, 128, 10738-10744 M. Swart, M. Sol and F.M. Bickelhaupt "Energy landscapes of nucleophilic substitution (SN2) reactions: A comparison of density functional theory and coupled cluster methods" J. Comput. Chem. 2007, accepted for publication ------------------------------------------ I am coauthor of the papers for the M05 and M06 method. You can use the NWChem program and the attached patch to run calculations with the M05 and M06 functionals. You can download the NWChem-v.5.0 program from http://www.emsl.pnl.gov/docs/nwchem/nwchem.html.For the basis set, you may want to try the DZQ or TZQ basis sets;they are described in two papers: N. Schultz, Y. Zhao, and D. G. Truhlar, J. Phys. Chem. A 109, 4388 (2005). N. E. Schultz, B. F. Gherman, C. J. Cramer, and D. G. Truhlar, J. Phys. Chem. B (2006). Yan ------------------------------------------- The SDD ECP is a reliable basis set for transition metals. By default it is the D95 basis set which is assigned to the non-metallic element if you specify SDD as the basis set. For more reliable results I would use D95* instead of D95. With G98 (not sure about G03) I would specify in the input card something like 'B3LYP/SDD extrabasis' You have to include the polarization function data in the input file for the atoms other than Ru. You can obtain the basis set details using the keyword 'gfprint' Wai-To Chan ------------------------------------------- I am currently performing calculations on organometallics using Gaussian03 with different DFT functionals. In my experience, the MPW1K functional gives good results in calculating reaction barriers. You can find the route section for G03 in the Truhlar website: http://comp.chem.umn.edu/info/DFT.htm In this paper, you will find an interesting comparison of different DFT methods applied to the study of barrier heights for different reactions: J. Phys. Chem. A, 108, 7621 (2004). Good luck, Otello ------------------------------------------- From owner-chemistry@ccl.net Tue Feb 6 19:00:00 2007 From: "Richard L Wood rwoodphd{:}msn.com" To: CCL Subject: CCL: Molegro Message-Id: <-33549-070206185805-7840-WYXd0PHle5xilLBvxRHofA*_*server.ccl.net> X-Original-From: "Richard L Wood" Date: Tue, 6 Feb 2007 18:58:02 -0500 Sent to CCL by: "Richard L Wood" [rwoodphd ~ msn.com] Hi all, I've just started using Molegro to dock ligands to proteins and I am having some difficulty. I can import a protein alright, but when I import a ligand (which is a small peptide in this case), it calls it a protein. So, I have two proteins and no ligands. Is there a way in Molegro that I can trick it into seeing my peptide as a ligand so that I can dock it? TIA, Richard From owner-chemistry@ccl.net Tue Feb 6 20:34:00 2007 From: "Richard Leo Wood rwoodphd*|*msn.com" To: CCL Subject: CCL: Molegro Message-Id: <-33550-070206202956-12623-ZcdsQ4KBQdws4tc6NHn4Ng[#]server.ccl.net> X-Original-From: "Richard Leo Wood" Date: Tue, 6 Feb 2007 20:29:52 -0500 Sent to CCL by: "Richard Leo Wood" [rwoodphd###msn.com] Hi all, Actually, I found my own workaround, as I usually do. Take the peptide (as a pdb file), convert it to an xyz file. Change the unknown atoms to teh correct ones, then convert this to a mol format file. Then import the mol file into Molegro and do the docking calculations. Richard From: "Richard L Wood rwoodphd{:}msn.com" Reply-To: "CCL Subscribers" To: "Wood, Richard L. -id3m4-" Subject: CCL: Molegro Date: Tue, 6 Feb 2007 18:58:02 -0500 Sent to CCL by: "Richard L Wood" [rwoodphd ~ msn.com] Hi all, I've just started using Molegro to dock ligands to proteins and I am having some difficulty. I can import a protein alright, but when I import a ligand (which is a small peptide in this case), it calls it a protein. So, I have two proteins and no ligands. Is there a way in Molegro that I can trick it into seeing my peptide as a ligand so that I can dock it? TIA, Richard