From owner-chemistry@ccl.net Mon Aug 16 05:45:01 2010 From: "Paolo Tosco paolo.tosco,unito.it" To: CCL Subject: CCL: Open3DQSAR 1.3 released Message-Id: <-42525-100816054246-13030-DqdveY7D7AWtyZekbSnvtA~!~server.ccl.net> X-Original-From: "Paolo Tosco" Date: Mon, 16 Aug 2010 05:42:44 -0400 Sent to CCL by: "Paolo Tosco" [paolo.tosco ~~ unito.it] Dear CCLers, Open3DQSAR 1.3 has been released: http://www.open3dqsar.org Open3DQSAR is an open-source software aimed at pharmacophore exploration of a set of ligands endowed with biological activity by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRID and CoMFA/CoMSIA MIFs. On these MIFs, Open3DQSAR performs fast, automated PLS chemometric analysis allowing to quickly generate and challenge the predictivity of many 3D-QSAR models using different training/test set combinations, superposition schemes, variable selection and data scrambling procedures, etc. High computational performance is attained through implementation of parallelized algorithms for MIF generation, PLS model building and validation, variable selection. Open3DQSAR 1.3, with respect to version 1.2, allows direct generation of Molecular Discovery GRID MIFs, by assigning GRID force field atom types and subsequently calling GRIN and GRID programs to generate the fields. Until version 1.2, it was necessary to manually generate the fields in GREATER, then import them into Open3DQSAR. Removing this interactive step allows for easier automated generation/evaluation of a number of different models. Further improvements and bug fixes are detailed in the ChangeLog. Feedback and suggestions for future versions are very welcome. Open3DQSAR runs on all mainstream operating systems (Windows 32/64-bit, Linux 32/64-bit, Solaris x86 32/64-bit, Intel Mac OS X 32/64-bit). Open3DQSAR is available free of charge to eligible users according to the license terms; for information, see http://www.open3dqsar.org Tosco, P.; Balle, T. "Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields", J. Mol. Model. 2010 http://dx.doi.org/10.1007/s00894-010-0684-x Kind regards, Paolo Tosco Department of Drug Science and Technology Faculty of Pharmacy, University of Turin Via Pietro Giuria 9, 10125 Torino, Italy Thomas Balle Department of Medicinal Chemistry The Faculty of Pharmaceutical Sciences, University of Copenhagen, 2 Universitetsparken, 2100 Copenhagen, Denmark From owner-chemistry@ccl.net Mon Aug 16 08:21:01 2010 From: "Sandhya Rai sandhyachemistry30,,gmail.com" To: CCL Subject: CCL: problem in running the MP2 calculations Message-Id: <-42526-100816063216-8481-rl53W/IfJH0c7jMcFnyjkg]![server.ccl.net> X-Original-From: Sandhya Rai Content-Type: multipart/alternative; boundary=e0cb4e88781159e396048dee58bb Date: Mon, 16 Aug 2010 19:32:10 +0900 MIME-Version: 1.0 Sent to CCL by: Sandhya Rai [sandhyachemistry30%gmail.com] --e0cb4e88781159e396048dee58bb Content-Type: text/plain; charset=ISO-8859-1 Hi! I have been doing the MP2 calculations on a system of amino acids incorporated with gold molecules but my optimization job terminates saying 'small coeff. for last iteration. I can't understand what it means & the same molecule gets optimized using DFT. Plz help me -- Sandhya Rai Persuing Ph.D Centre of Computational Natural Sciences & Bioinformatics International Institute of Information & Technology Gachibowli, Hyderabad. --e0cb4e88781159e396048dee58bb Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi!
I have been doing the MP2 calculations on a system of amino acids in= corporated with gold molecules but my optimization job terminates saying &#= 39;small coeff. for last iteration. I can't understand what it means &a= mp; the same molecule gets optimized using DFT.
=A0Plz help me

--
Sandhya Rai
Persuing Ph.D
= Centre of Computational Natural Sciences & Bioinformatics
Internatio= nal Institute of Information & Technology
Gachibowli, Hyderabad.

--e0cb4e88781159e396048dee58bb-- From owner-chemistry@ccl.net Mon Aug 16 08:56:01 2010 From: "Honman Yau honman.yau*student.unsw.edu.au" To: CCL Subject: CCL: Problem with Geometry Optimisation using PCM Message-Id: <-42527-100816063158-7163-lbfEz6gawauIZ6g78jPxAA..server.ccl.net> X-Original-From: "Honman Yau" Date: Mon, 16 Aug 2010 06:31:56 -0400 Sent to CCL by: "Honman Yau" [honman.yau#student.unsw.edu.au] Dear all, I have been trying to run a geometry optimisation on a pair of para- substituted aryl diazonium salt, one of which a dication (p-trimethylamino) and the other a zwitterion (p-sulfonate), without much success. The ultimate goal is to look at the change in charge distribution (and perhaps the LUMOs) with and without the interaction between the pair. After searching for possible solutions on forums, blogs and mailing lists including everything I could find on CCL...) for a couple of weeks (and tried different things in between) I have now reached the point where I think that I must be doing something silly and it would be lovely if someone could point out a mistake (or two, or more... such as using other solvation models?), provide suggestions on tackling the problem, or suggest alternatives (or all of the above!). As an aside, after looking for similar studies in the literature, it appears that some people just simply take their gas phase optimsied structures and, without further geometry optimisation in a PCM, do subsequent calculations with them in PCM - is this generally acceptable? I personally find that quite strange and cannot justify it (apart from the fact that it may cause sleep deprivation). The following is, in chronological order, what I have attempted so far: N.B. For all of the calculations below I specified the charge of the system as +2 and multiplicity as 1. Geometry optimisation of the pair in the gas phase completed without hassles, resulting in an end-on interaction of the sulfonate group with a slightly bent dication. Frequency calculation was then performed on the optimised structure; no imaginary frequencies were found in a frequency calculation. Using this structure, geometry optimisation with the following route card was performed with: #P B3LYP/6-31G* OPT SCRF=(PCM,Solvent=Acetonitrile) The job often just abnormally terminated without any error messages and never converged even after a few OPT=Restart. Frequency calculations using the route card: #P B3LYP/6-31G* FREQ SCRF=(PCM,Solvent=Acetonitrile) returned a few imaginary frequencies, mostly rotation of the aromatic ring bearing the sulfonate functionality and bending-like movements of the species - all about the center of interaction. > From there I tried modifying the starting structure slightly a couple of times, but to no avail. Smaller or larger basis sets and OPT=gdiis did not help either. I thought perhaps it could be a problem with PCM and after digging around the web for a bit I tried again with: #P B3LYP/6-31+G* OPT=(maxcycle=512) SCRF=(Read,PCM,Solvent=Acetonitrile) Geom=Allcheckpoint . OFac=0.8 RMin=0.5 The job ran a bit better (did not stop without warning) but the energies kept cycling and failed to converge. So I tried again with: #P B3LYP/6-31+G* OPT=(maxcycle=512) SCRF=(Read,PCM,Solvent=Acetonitrile) NOSYMM . OFac=0.8 RMin=0.5 NOSYMMCAV When it failed to converge for the first time, I did a frequency calculation then optimised again with ReadFC: #P B3LYP/6-31+G* OPT=(ReadFC,maxcycle=512) SCRF=(Read,PCM,Solvent=Acetonitrile) NOSYMM . OFac=0.8 RMin=0.5 NOSYMMCAV Then the job eventually converged with (finally!) a normal termination. Unfortunately when I did a frequency calculation: #P B3LYP/6-31+G* FREQ SCRF=(Read,PCM,Solvent=Acetonitrile) NOSYMM . OFac=0.8 RMin=0.5 NOSYMMCAV I got five imaginary frequencies... :( That pretty much sums up what I have done so far. Thank you very much in advance for any suggestions! Kind regards, Honman School of Chemistry University of New South Wales Sydney NSW 2052 Australia Contact e-mail: honman.yau{}student.unsw.edu.au From owner-chemistry@ccl.net Mon Aug 16 09:31:01 2010 From: "Sayed Mesa elsayed.elmes|a|yahoo.com" To: CCL Subject: CCL:G: COSMO-RS, enthalpy and free energy of complexation Message-Id: <-42528-100816083650-31458-T08lkNJdpyCC7L2T68jD7A*server.ccl.net> X-Original-From: "Sayed Mesa" Date: Mon, 16 Aug 2010 08:36:49 -0400 Sent to CCL by: "Sayed Mesa" [elsayed.elmes*yahoo.com] Dear Gaussian community I am calculating the enthalpy and free energy for complexation reaction between transition metal with chelate ligand (has four N-atoms for coordination) in both gas phase and solvent (COSMO-RS). In both cases I used tetrasolvated cluster of water molecules around the transition metal (i.e. bare metal is not used). So the reaction will be: L + [M(H2O)4]2+ ---- [ML]2+ + 4H2O (either in gas or in solvent). I have two questions; the first: is this scenario is right? If yes please confirm me by a reference if possible. The second question, is I need to do geometry optimization for reactants and products again in solvent or single point calculations is enough for calculating the enthalpy and free energy for complexation? Thanks in advance Sayed From owner-chemistry@ccl.net Mon Aug 16 10:57:00 2010 From: "Jerome Kieffer Jerome.Kieffer]_[terre-adelie.org" To: CCL Subject: CCL: Problem with Geometry Optimisation using PCM Message-Id: <-42529-100816104615-13276-ohTMDcEkEI7Db1DhoCF7Pg:_:server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Mon, 16 Aug 2010 16:45:54 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [Jerome.Kieffer##terre-adelie.org] Hi, The oscillation you encounter in energy could be related to some electron density that "escapes" in the solvent. Using a CPCM (COSMO) solvataion scheme can help: as the solvant behaves as a metal, residual electron density is bushed back towards the molecule (and does not escape) Hope this helps. -- Jerome Kieffer From owner-chemistry@ccl.net Mon Aug 16 15:42:00 2010 From: "Stephen P. Molnar s.molnar*o*sbcglobal.net" To: CCL Subject: CCL: Open3DQSAR 1.3 released Message-Id: <-42530-100816145706-8259-Lh9yi+piO4Sj3vi0u1VM3w^server.ccl.net> X-Original-From: "Stephen P. Molnar" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Mon, 16 Aug 2010 15:02:28 -0400 Mime-Version: 1.0 Sent to CCL by: "Stephen P. Molnar" [s.molnar##sbcglobal.net] Every browser that I use has the left side of your web pages blocing the main window. This makes it impossible to submit the registration form as all of the titles of the fields. What information do you require for registration? Thanks in advance -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivarate http://www.FoundationForChemistry.com On Mon, 16 Aug 2010 05:42:44 -0400 "Paolo Tosco paolo.tosco,unito.it" wrote: > > Sent to CCL by: "Paolo Tosco" [paolo.tosco ~~ unito.it] > Dear CCLers, > > Open3DQSAR 1.3 has been released: > > http://www.open3dqsar.org > > Open3DQSAR is an open-source software aimed at pharmacophore > exploration of a set of ligands endowed with biological activity by > high-throughput chemometric analysis of molecular interaction fields > (MIFs). > > Open3DQSAR can generate steric potential, electron density and > MM/QM electrostatic potential fields; furthermore, it can import > GRID and CoMFA/CoMSIA MIFs. > On these MIFs, Open3DQSAR performs fast, automated PLS chemometric > analysis allowing to quickly generate and challenge the predictivity > of many 3D-QSAR models using different training/test set > combinations, superposition schemes, variable selection and data > scrambling procedures, etc. High computational performance is > attained through implementation of parallelized algorithms for MIF > generation, PLS model building and validation, variable selection. > > Open3DQSAR 1.3, with respect to version 1.2, allows direct generation > of Molecular Discovery GRID MIFs, by assigning GRID force field atom > types and subsequently calling GRIN and GRID programs to generate the > fields. Until version 1.2, it was necessary to manually generate the > fields in GREATER, then import them into Open3DQSAR. Removing this > interactive step allows for easier automated generation/evaluation of > a number of different models. Further improvements and bug fixes are > detailed in the ChangeLog. Feedback and suggestions for future > versions are very welcome. > > Open3DQSAR runs on all mainstream operating systems (Windows > 32/64-bit, Linux 32/64-bit, Solaris x86 32/64-bit, Intel Mac OS X > 32/64-bit). > Open3DQSAR is available free of charge to eligible users according > to the license terms; for information, see > > http://www.open3dqsar.org > > Tosco, P.; Balle, T. "Open3DQSAR: a new open-source > software aimed at high-throughput chemometric analysis > of molecular interaction fields", J. Mol. Model. 2010 > http://dx.doi.org/10.1007/s00894-010-0684-x > > Kind regards, > > Paolo Tosco > Department of Drug Science and Technology > Faculty of Pharmacy, University of Turin > Via Pietro Giuria 9, 10125 Torino, Italy > > > Thomas Balle > Department of Medicinal Chemistry > The Faculty of Pharmaceutical Sciences, University of Copenhagen, > 2 Universitetsparken, 2100 Copenhagen, Denmark > > -- From owner-chemistry@ccl.net Mon Aug 16 17:30:01 2010 From: "Ronald Bakus rbakus[a]chem.ucsb.edu" To: CCL Subject: CCL:G: Retriving scf from optimization for multistep job Message-Id: <-42531-100816172918-25174-FRy10eX8okL0JrfiTU3gAw^^^server.ccl.net> X-Original-From: "Ronald Bakus" Date: Mon, 16 Aug 2010 17:29:16 -0400 Sent to CCL by: "Ronald Bakus" [rbakus!=!chem.ucsb.edu] I know that this question has to have been asked before, but for the life of me, I cant find it on ccl, so Ill ask it. If I'm doing a multistep job in Gaussian 03 (say geometry optimization followed by TDDFT) in the first step, it will go through several cycles of converging the SCF and finally reach the local minima, with the converged scf. In the second step, it will do another SCF cycle and reconverge the SCF, and then do the TDDFT calculation. Is there a keyword that can be used to pass the converged SCF from the first step to the second step TDDFT calculation so that I don't waste CPU time? In example: .. #p opt B3LYP/6-311+G(d,p) geom=connectivity formcheck --Link1-- .. #p td B3LYP/6-311+G(d,p) KEYWORD guess=check geom=allcheck formcheck Thanks -Ron From owner-chemistry@ccl.net Mon Aug 16 21:01:01 2010 From: "willsd{=}appstate.edu" To: CCL Subject: CCL:G: Retriving scf from optimization for multistep job Message-Id: <-42532-100816205020-11106-WOUg5Q6ah49O61CwHMBWrg+/-server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 17 Aug 2010 00:44:30 GMT MIME-Version: 1.0 Sent to CCL by: [willsd%x%appstate.edu] Try guess=read rather than guess=check. Steve Williams ----- Original Message ----- > From: "Ronald Bakus rbakus[a]chem.ucsb.edu" Date: Monday, August 16, 2010 6:48 pm Subject: CCL:G: Retriving scf from optimization for multistep job To: "Williams, Steve " > > Sent to CCL by: "Ronald Bakus" [rbakus!=!chem.ucsb.edu] > I know that this question has to have been asked before, but for > the life of me, I cant find it on ccl, so Ill ask it. If I'm doing > a multistep job in Gaussian 03 (say geometry optimization followed > by TDDFT) in the first step, it will go through several cycles of > converging the SCF and finally reach the local minima, with the > converged scf. In the second step, it will do another SCF cycle > and reconverge the SCF, and then do the TDDFT calculation. Is > there a keyword that can be used to pass the converged SCF from the > first step to the second step TDDFT calculation so that I don't > waste CPU time? > > In example: > .. > #p opt B3LYP/6-311+G(d,p) geom=connectivity formcheck > > --Link1-- > .. > #p td B3LYP/6-311+G(d,p) KEYWORD guess=check geom=allcheck formcheck > > > > Thanks > -Ron > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the |-| sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Mon Aug 16 22:38:01 2010 From: "Ronald Bakus rbakus() chem.ucsb.edu" To: CCL Subject: CCL:G: Retriving scf from optimization for multistep job Message-Id: <-42533-100816223656-25067-/ws2SSRqiP65exaQvvo08w]![server.ccl.net> X-Original-From: "Ronald Bakus" Date: Mon, 16 Aug 2010 22:36:54 -0400 Sent to CCL by: "Ronald Bakus" [rbakus{}chem.ucsb.edu] That was a typo on my part when I typed that up. guess=read, afaik, just reads in the inital guess from the checkpoint before it initiates scf. > "willsd{=}appstate.edu" wrote: > > Sent to CCL by: [willsd%x%appstate.edu] > Try guess=read rather than guess=check. > Steve Williams > > ----- Original Message ----- > > From: "Ronald Bakus rbakus[a]chem.ucsb.edu" > Date: Monday, August 16, 2010 6:48 pm > Subject: CCL:G: Retriving scf from optimization for multistep job > To: "Williams, Steve " > > > > > Sent to CCL by: "Ronald Bakus" [rbakus!=!chem.ucsb.edu] > > I know that this question has to have been asked before, but for > > the life of me, I cant find it on ccl, so Ill ask it. If I'm doing > > a multistep job in Gaussian 03 (say geometry optimization followed > > by TDDFT) in the first step, it will go through several cycles of > > converging the SCF and finally reach the local minima, with the > > converged scf. In the second step, it will do another SCF cycle > > and reconverge the SCF, and then do the TDDFT calculation. Is > > there a keyword that can be used to pass the converged SCF from the > > first step to the second step TDDFT calculation so that I don't > > waste CPU time? > > > > In example: > > .. > > #p opt B3LYP/6-311+G(d,p) geom=connectivity formcheck > > > > --Link1-- > > .. > > #p td B3LYP/6-311+G(d,p) KEYWORD guess=check geom=allcheck formcheck > > > > > > > > Thanks > > -Ron > > > > > > > > -= This is automatically added to each message by the mailing > > script =- > > To recover the email address of the author of the message, please > > changethe strange characters on the top line to the |-| sign. You can > > also> Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/> > > > > > > From owner-chemistry@ccl.net Mon Aug 16 23:13:00 2010 From: "=?GB2312?B?0vO9oQ==?= janeyin600]=[gmail.com" To: CCL Subject: CCL:G: GEN doesn't work Message-Id: <-42534-100816224956-5786-g9sKEnK9uqFRADQRa4d2bg],[server.ccl.net> X-Original-From: =?GB2312?B?0vO9oQ==?= Content-Type: multipart/alternative; boundary=0016e64806789f86f4048dfc0001 Date: Mon, 16 Aug 2010 21:49:48 -0500 MIME-Version: 1.0 Sent to CCL by: =?GB2312?B?0vO9oQ==?= [janeyin600(0)gmail.com] --0016e64806789f86f4048dfc0001 Content-Type: text/plain; charset=ISO-8859-1 Hi there, I had a GEN error in my Gaussian output. This is my input: * # B3LYP/GEN OPT PSEUDO=READ * ** *molecule specification* *N C H O 0 6-31G(d) **** Fe 0 6-311+G* **** Fe 0 6-311+G** And this is the end of my output: *Unrecognized potential number 6 in GetPot.* *Error termination via Lnk1e in /usr/local/g03/l301.exe at Sat Aug 14 21:08:16 2010.* Does anyone know what the "unrecognized potential number" means in here? Thank you very much! Jane ** --0016e64806789f86f4048dfc0001 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi there,
=A0
I had a GEN error in my=A0Gaussian output.
=A0
This is my input:
=A0# B3LYP= /GEN OPT PSEUDO=3DREAD
<= /font>=A0
molecule s= pecification

N C H O 06-31G(d)
****
Fe 0
6-311+G*
****
=A0=A0
Fe 0
6-311+G= *


And this is the end of my output:
Unrecognized potential number 6 in GetPot.=

Error termination via Lnk1e in= /usr/local/g03/l301.exe at Sat Aug 14 21:08:16 2010.

Does anyone know what the "unrecognized potential=A0number" = means=A0in here?=A0
Thank you very much!
=A0
Jane

=A0

--0016e64806789f86f4048dfc0001-- From owner-chemistry@ccl.net Mon Aug 16 23:47:01 2010 From: "N. Sukumar nagams,+,rpi.edu" To: CCL Subject: CCL:G: Retriving scf from optimization for multistep job Message-Id: <-42535-100816232833-8905-tuBSF9fsUooJQWlnT6wr2w[A]server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Mon, 16 Aug 2010 23:28:27 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams _ rpi.edu] Density=Checkpoint recovers the density from the checkpoint file for analysis: the calculation does not recompute new integrals, SCF, etc. Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research http://reccr.chem.rpi.edu/ -------------------------- "It is nice to know that the computer understands the problem. But I would like to understand it too." -- Eugene P. Wigner ==============Original message text=============== On Mon, 16 Aug 2010 22:36:54 EDT "Ronald Bakus rbakus() chem.ucsb.edu" wrote: Sent to CCL by: "Ronald Bakus" [rbakus{}chem.ucsb.edu] That was a typo on my part when I typed that up. guess=read, afaik, just reads in the inital guess from the checkpoint before it initiates scf. > "willsd{=}appstate.edu" wrote: > > Sent to CCL by: [willsd%x%appstate.edu] > Try guess=read rather than guess=check. > Steve Williams > > ----- Original Message ----- > > From: "Ronald Bakus rbakus[a]chem.ucsb.edu" > Date: Monday, August 16, 2010 6:48 pm > Subject: CCL:G: Retriving scf from optimization for multistep job > To: "Williams, Steve " > > > > > Sent to CCL by: "Ronald Bakus" [rbakus!=!chem.ucsb.edu] > > I know that this question has to have been asked before, but for > > the life of me, I cant find it on ccl, so Ill ask it. If I'm doing > > a multistep job in Gaussian 03 (say geometry optimization followed > > by TDDFT) in the first step, it will go through several cycles of > > converging the SCF and finally reach the local minima, with the > > converged scf. In the second step, it will do another SCF cycle > > and reconverge the SCF, and then do the TDDFT calculation. Is > > there a keyword that can be used to pass the converged SCF from the > > first step to the second step TDDFT calculation so that I don't > > waste CPU time? > > > > In example: > > .. > > #p opt B3LYP/6-311+G(d,p) geom=connectivity formcheck > > > > --Link1-- > > .. > > #p td B3LYP/6-311+G(d,p) KEYWORD guess=check geom=allcheck formcheck > > > > > > > > Thanks > > -Ron > > > > > > > > -= This is automatically added to each message by the mailing > > script =- > > To recover the email address of the author of the message, please > > changethe strange characters on the top line to the |-| sign. You can > > also> Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========