From owner-chemistry@ccl.net Mon Apr 5 00:53:00 2010 From: "Uttama Mukherjee uttamachemistry:gmail.com" To: CCL Subject: CCL:G: ION PAIR OPTIMIZATION Message-Id: <-41594-100404144344-22682-Qda366XXAoDy4vYlBWwkIA,,server.ccl.net> X-Original-From: "Uttama Mukherjee" Date: Sun, 4 Apr 2010 14:43:43 -0400 Sent to CCL by: "Uttama Mukherjee" [uttamachemistry]![gmail.com] Hello, I just wanted to know how do we optimize ion pairs using Gaussian03 suit of programmes. Is there any minimum bond distance that we have to maintain so that the two species(cation & anion) remain as ions in the optimized stucture? As I'm submitting the job(after optimization of cation & anion individually), for optimization of the ion pair as a whole, the output always shows the neutral pair(one H transferred)and it no longer remains as ion. So my question is, what do I've to do to maintain them as ion? Please help. Thanks & regards, Uttama Mukherjee, uttamachemistry:-:gmail.com From owner-chemistry@ccl.net Mon Apr 5 05:24:00 2010 From: "Gijs Schaftenaar schaft{=}cmbi.ru.nl" To: CCL Subject: CCL:G: Converting Gaussian .log NMR output to .jdx format Message-Id: <-41595-100404093940-1754-EEHYao/OGjctcXuO9i3fkQ|server.ccl.net> X-Original-From: Gijs Schaftenaar Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Sun, 4 Apr 2010 14:36:54 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Gijs Schaftenaar [schaft++cmbi.ru.nl] Dear Robert, Molden4.9 can visualise calculated spin-spin couplings from gaussian. Best Regards, Gijs Schaftenaar +----------------------------------------------------------------+ Gijs Schaftenaar, Dr. | Computational Drug Discovery, CMBI Email: | Radboud University of Nijmegen G.Schaftenaar+*+ncmls.ru.nl | Medical Centre / NCMLS, route 260 Tel. : +31 24 3619674 | Geert-Grooteplein 28 Fax : +31 24 3619395 | 6525 GA Nijmegen, The Netherlands +----------------------------------------------------------------+ On Sat, 3 Apr 2010, Robert V. Kolakowski robertk%%scripps.edu wrote: > Date: Sat, 3 Apr 2010 13:00:31 -0400 > From: Robert V. Kolakowski robertk%%scripps.edu > Reply-To: CCL Subscribers > To: "Schaftenaar, Gijs " > Subject: CCL:G: Converting Gaussian .log NMR output to .jdx format > > > Sent to CCL by: "Robert V. Kolakowski" [robertk-*-scripps.edu] > Good Day, > > Has anyone out there found an off the shelf solution for > converting Gaussian *.log NMR output to the universal > *.jdx format? > > I'm trying to visualize calculated spin-spin couplings. > > Any help would be welcome. > > Cheers, > > Robert V. Kolakowski, Ph.D. > The Scripps Research Institute > La Jolla, CA, 92037 > robertk],[scripps.edu> > From owner-chemistry@ccl.net Mon Apr 5 05:59:00 2010 From: "yahoo.com" To: CCL Subject: CCL:G: Convert out-file to chk-file Message-Id: <-41596-100405012935-21475-uLKFsMDRELJaYPQRwkrGLA(0)server.ccl.net> X-Original-From: ~ yahoo.com> Content-Type: multipart/alternative; boundary="0-366495115-1270442049=:62179" Date: Sun, 4 Apr 2010 21:34:09 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: {:}yahoo.com] --0-366495115-1270442049=:62179 Content-Type: text/plain; charset=us-ascii Hi, If you have Gaussian Soft. then you can find the molecular system together with all other parameters, route section, etc. in the out file. So you can do the simulation again to create .chk- file you need. I hope this helps. Regards, ________________________________ > From: Pavel DUB pavel.dub(-)lcc-toulouse.fr To:,yahoo.com> Sent: Sun, April 4, 2010 10:14:20 PM Subject: CCL: Convert out-file to chk-file Sent to CCL by: "Pavel DUB" [pavel.dub**lcc-toulouse.fr] Hello! I need to calculate thermoparameters at 423K and for this I need to use freqchk option via the original chk-file. Unfortunetely, I have only the out-files. Is it possible to generate chk-files somehow? Thank you Pavel DUB, PhD, CNRS, Francehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-366495115-1270442049=:62179 Content-Type: text/html; charset=us-ascii
Hi,
If you have Gaussian Soft. then you can find the molecular system together with all other parameters, route section, etc. in the out file. So you can do the simulation again to create .chk- file you need.

I hope this helps.
Regards,

From: Pavel DUB pavel.dub(-)lcc-toulouse.fr <owner-chemistry,ccl.net>
To: "m>
Sent: Sun, April 4, 2010 10:14:20 PM
Subject: CCL: Convert out-file to chk-file


Sent to CCL by: "Pavel  DUB" [pavel.dub**lcc-toulouse.fr]
Hello!
I need to calculate thermoparameters at 423K and for this I need to use freqchk option via the original chk-file. Unfortunetely, I have only the out-files. Is it possible to generate chk-files somehow?
Thank you
Pavel DUB, PhD, CNRS, France



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--0-366495115-1270442049=:62179-- From owner-chemistry@ccl.net Mon Apr 5 09:05:00 2010 From: "Close, David M. CLOSED:+:mail.etsu.edu" To: CCL Subject: CCL:G: Convert out-file to chk-file Message-Id: <-41597-100405081949-16942-3FGNnPUlwe5pwOlFssdnsQ#,#server.ccl.net> X-Original-From: "Close, David M." Content-Class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Mon, 5 Apr 2010 07:50:22 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED*mail.etsu.edu] Pavel: Freqchk is a utility that converts information from a .chk file. Since you don't have a .chk file, you will have to generate one. In the input file, just add a line that says %chk=3Dfilename.chk. When you are done running the program there will be a filename.chk file in the output. It is in binary and can't be read. The Gaussian manuel, in the utility section shows how to use formchk and freqchk. Regards, Dave Close.=20 -----Original Message----- > From: owner-chemistry+closed=3D=3Detsu.edu ~ ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu ~ ccl.net] On Behalf Of Pavel = DUB pavel.dub(-)lcc-toulouse.fr Sent: Sunday, April 04, 2010 1:44 PM To: Close, David M. Subject: CCL: Convert out-file to chk-file Sent to CCL by: "Pavel DUB" [pavel.dub**lcc-toulouse.fr] Hello! I need to calculate thermoparameters at 423K and for this I need to use freqchk option via the original chk-file. Unfortunetely, I have only the out-files. Is it possible to generate chk-files somehow? Thank you Pavel DUB, PhD, CNRS, France -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Apr 5 10:56:00 2010 From: "david.anick*|*rcn.com" To: CCL Subject: CCL: Convert out-file to chk-file Message-Id: <-41598-100405092750-29979-EQwFv3o0Kmc6bEgkcRRNCg{}server.ccl.net> X-Original-From: Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Mon, 5 Apr 2010 08:55:32 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: [david.anick() rcn.com] Dear Pavel, Assuming that your .out file includes the results of a FREQ calculation at the optimized geometry, you can compute thermodynamic quantities at any temperature you like using the perl script, thermo.pl Go to http://www.nist.gov/cstl/chemical_properties/computational/thermochemistry_script.cfm where you can use this script on-line by uploading your .out file. Peace, David Anick ---- Original message ---- >Date: Sun, 4 Apr 2010 13:44:20 -0400 >From: "Pavel DUB pavel.dub(-)lcc-toulouse.fr" >Subject: CCL: Convert out-file to chk-file >To: "Anick, David " > > >Sent to CCL by: "Pavel DUB" [pavel.dub**lcc-toulouse.fr] >Hello! >I need to calculate thermoparameters at 423K and for this I need to use freqchk option via the original chk-file. Unfortunetely, I have only the out-files. Is it possible to generate chk-files somehow? >Thank you >Pavel DUB, PhD, CNRS, France> > From owner-chemistry@ccl.net Mon Apr 5 12:17:00 2010 From: "Jamin Krinsky jamink]=[berkeley.edu" To: CCL Subject: CCL:G: ION PAIR OPTIMIZATION Message-Id: <-41599-100405121552-13205-D7u3/xqXYxPsDvoyf8UYrQ:_:server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 5 Apr 2010 09:15:40 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink^berkeley.edu] Dear Uttama, Assuming you did not place the protonated moiety too close to the basic site on the counterion (closer than the proton's bond with the acidic site), that calculation is telling you that there is no minimum-energy structure at the protonation state you desire, at least at that level of theory. As for specifying constraints on cation-anion distance, then you would not really be optimizing the system. Relative protonation energies can change quite a bit with environment, so you might try using an implicit solvent model such as PCM (default solvation) or CPCM (like COSMO). The solvent to use depends on what you want to know, but water would be a good place to start, to see if there is any affect. You'd add "scrf(solvent=3Dwater)" to your route section, for the PCM model. Regards, Jamin On Sun, Apr 4, 2010 at 11:43 AM, Uttama Mukherjee uttamachemistry:gmail.com wrote: > > Sent to CCL by: "Uttama =A0Mukherjee" [uttamachemistry]![gmail.com] > Hello, I just wanted to know how do we optimize ion pairs using Gaussian0= 3 suit > of programmes. Is there =A0any minimum bond distance that we have to main= tain so > that the two species(cation & anion) remain as ions in the optimized stuc= ture? > =A0 As I'm submitting the job(after optimization of cation & anion > individually), for optimization of the ion pair as a whole, the output al= ways > shows the neutral pair(one H transferred)and it no longer remains as ion.= So my > question is, what do I've to do to maintain them as ion? Please help. > Thanks & regards, > Uttama Mukherjee, > uttamachemistry ~ gmail.com > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink ~ berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Mon Apr 5 15:10:01 2010 From: "Brian B Masek brian.masek^^certara.com" To: CCL Subject: CCL: Announcing SYBYL-X 1.1 Message-Id: <-41600-100405132513-32385-jESpMT0ZB3KDTh5oF+Kefw_-_server.ccl.net> X-Original-From: "Brian B Masek" Date: Mon, 5 Apr 2010 13:24:58 -0400 Sent to CCL by: "Brian B Masek" [brian.masek===certara.com] Dear CCL Colleagues SYBYL-X 1.1, the next generation of the SYBYL molecular modeling suite, is available for immediate download on Windows and Linux for all supported customers and evaluators. If you havent used SYBYL in a while, now is the time to take a fresh look. SYBYL-X 1.1 represents a major step to make your molecular design research more efficient and pleasurable. Performing routine tasks with SYBYL-X is now faster and easier than ever. You will notice many improved possibilities for the basic use of SYBYL-X. Particularly noteworthy are: a new selection model that allows actions on selected entities; enhanced, simplified menu systems for frequently used functions; significantly updated toolbar system; context sensitive (right-click) menus; and enhanced session saving capabilities. SYBYL-X 1.1 provides significant enhancements in general usability, reducing by half the number of mouse clicks and by more than half the mouse travel needed for basic molecule visualization and manipulation, thereby providing a far more intuitive modeling experience. Youll also see workflow improvements, including the addition of protein preparation and ligand preparation to the docking/virtual screening workflows and addition of MOLCAD channel surfaces capabilities to active site location. Scientific improvements in SYBYL-X 1.1s updated Surflex-Dock version include treatment of protein flexibility in docking and an intramolecular self-scoring term in docking scoring. We encourage all current customers to download and migrate to SYBYL-X 1.1 today, and begin taking advantage of the latest productivity improvements from Tripos the release is available at www.tripos.com/download in the SYBYL section. If youd like to evaluate SYBYL-X, go to www.tripos.com and request an evaluation today! Brian Masek Product Manager and Lead Scientist brian.masek : certara.com 314-951-3409 (office) 314-422-7849 (cell) ________________________________________ SYBYL-X 1.1, next generation molecular modeling software - newly redesigned - now available for Linux and Windows ! http://www.tripos.com/index.php?family=Modules,General.DownloadPortal,Browse&product=SYBYL ________________________________________ From owner-chemistry@ccl.net Mon Apr 5 15:45:01 2010 From: "Bahareh honarparvar bahareh_honarparvar : yahoo.com" To: CCL Subject: CCL:G: solvent effects Message-Id: <-41601-100405085047-18737-JuTdBQlAwEamcQk8duHl8A_._server.ccl.net> X-Original-From: Bahareh honarparvar Content-Type: multipart/alternative; boundary="0-1303423307-1270468238=:65232" Date: Mon, 5 Apr 2010 04:50:38 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Bahareh honarparvar [bahareh_honarparvar#%#yahoo.com] --0-1303423307-1270468238=:65232 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Emran Heshmati The most suitable solvation model for your biosystem is onsoger with scrf= =3Ddipole keyword. please let me know if you have any further information. Good luck B.Honarparvar --- On Sun, 4/4/10, Emran Heshmati heshmaty^^^yahoo.com wrote: > From: Emran Heshmati heshmaty^^^yahoo.com Subject: CCL:G: solvent effects To: "Honarparvar, Honarparvar " Date: Sunday, April 4, 2010, 2:43 PM Hi all=0AI want to optimize dipeptide structure in water solvent using DFT = method (G03 software). Which model (Onsager, PCM. IPCM, SCI-PCM and =E2=80= =A6) is more suitable for investigation the effect of solvent? =0A=C2=A0= =C2=A0=0ABest Regards Emran Heshmati P=C2=A0Save a tree... please don't print this e-mail unless you really need= to =0A Get your new Email address! =20 =0AGrab the Email name you've always wanted before someone else does!=0A=0A= =0A --0-1303423307-1270468238=:65232 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable =

Dear Emran Heshmati
Th= e most suitable solvation model for your biosystem is onsoger with scrf=3Dd= ipole keyword. please let me know if you have any further information.
G= ood luck
B.Honarparvar

--- On Sun, 4/4/10, Emran Heshmati hesh= maty^^^yahoo.com <owner-chemistry .. ccl.net> wrote:

From: Emran Heshmati heshmaty^^^yahoo.com <owner= -chemistry .. ccl.net>
Subject: CCL:G: solvent effects
To: "Honarparv= ar, Honarparvar " <bahareh_honarparvar .. yahoo.com>
Date: Su= nday, April 4, 2010, 2:43 PM

Hi all
=0A

I want to o= ptimize dipeptide structure in water solvent using DFT method (G03 software= ). Which model (Onsager, PCM. IPCM, SCI-PCM and =E2=80=A6) is more <= span style=3D"font-size: 10pt; font-family: Tahoma;">suitable for investiga= tion the effect of solvent? =0A

  
=0A
Best Regards
Emran Heshmati<= br>P Save a tree... please don't print this e-mail unless you rea= lly need to

=0A
Get your new Email address!
=0AGrab the Email name = you've always wanted before someone else does!

=0A=0A=0A=0A --0-1303423307-1270468238=:65232-- From owner-chemistry@ccl.net Mon Apr 5 18:08:01 2010 From: "Thanh N. Truong ttruong/a\astonis.com" To: CCL Subject: CCL: MolLib: A free interface for 3D structures of well-known molecules, fullerenes, and nanotubes Message-Id: <-41602-100405144645-23896-Nhfj0TOPKwmJ37usGVcJzQ.@.server.ccl.net> X-Original-From: "Thanh N. Truong" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0012_01CAD4B9.C2C1CEC0" Date: Mon, 5 Apr 2010 12:16:01 -0600 MIME-Version: 1.0 Sent to CCL by: "Thanh N. Truong" [ttruong(a)astonis.com] This is a multi-part message in MIME format. ------=_NextPart_000_0012_01CAD4B9.C2C1CEC0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit MolLib is a tool in Astonis App Catalog. It provides a convenient access to 3D structure of: 1. Well-known cyclic-hydrocarbons 2. amino acide residues 3. DNA/RNA bases 4. Sugars 5. database of fullerenes 6. user interface for TubeGen for creating nanotubes 7. User interface for the National Cancer Institute (NCI) small molecule database. You can use these 3D structures as starting point for editing or performing molecular modeling calculations using other tools in the Astonis App Catalog. MolLib also provides an excellent resource for learning about nano-materials such as fullerenes and nanotubes. Check out the features of MolLib here. http://www.astonis.com/tutorial/view?path=MolLib Also you can download Avisto and its tools at http://www.astonis.com ------=_NextPart_000_0012_01CAD4B9.C2C1CEC0 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

 

MolLib is a tool in Astonis App Catalog.  It = provides a convenient access to 3D structure of:

  1. Well-known = cyclic-hydrocarbons
  2. amino acide = residues
  3. DNA/RNA = bases
  4. Sugars
  5. database of = fullerenes
  6. user interface for = TubeGen for creating nanotubes
  7. User interface for the = National Cancer Institute (NCI) small molecule = database.

 

You can use these 3D structures as starting point for editing or performing molecular modeling calculations using other tools = in the Astonis App Catalog.  MolLib also provides an excellent resource = for learning about nano-materials such as fullerenes and = nanotubes.

 

Check out the features of MolLib here.  http://www.as= tonis.com/tutorial/view?path=3DMolLib

 

Also you can download Avisto and its tools at http://www.astonis.com

 

 

------=_NextPart_000_0012_01CAD4B9.C2C1CEC0-- From owner-chemistry@ccl.net Mon Apr 5 18:43:01 2010 From: "Volkan Ediz volkaned,,gmail.com" To: CCL Subject: CCL:G: Is it possible to convert sparkles to point charges? Message-Id: <-41603-100405145420-10104-T+Nwv5iGwiCuGP7BH5+Fkg^-^server.ccl.net> X-Original-From: "Volkan Ediz" Date: Mon, 5 Apr 2010 14:54:19 -0400 Sent to CCL by: "Volkan Ediz" [volkaned ~ gmail.com] Dear CCL users, I would like to run mopac calculations with external point charges. In G03, external point charges are not implemented to work with semi-empirical Hamiltonians and I would like to compare ab initio calculations with semi-empirical ones where my system is surrounded with external point charges, so I thought my best bet would be converting sparkles to point-charges. I'm aware that point charges and sparkles are not exactly the same thing and I couldn't find a decent source explaining the steps to convert sparkles to point charges. Is it possible? Your help would be greatly appreciated.