From owner-chemistry@ccl.net Tue Oct 5 00:37:00 2010 From: "Penny P Govender pennyg . uj.ac.za" To: CCL Subject: CCL: Conference Message-Id: <-42900-101005003240-11827-lf9JTXZ1wkgJpwvfis/z6Q(!)server.ccl.net> X-Original-From: "Penny P Govender" Date: Tue, 5 Oct 2010 00:32:39 -0400 Sent to CCL by: "Penny P Govender" [pennyg-x-uj.ac.za] Dear Colleagues You are invited to attend the 1st Advanced Materials Congress-2011 (www.am2011.ujn.edu.cn), jointly organized by the International Association of Advanced Materials (IAAM, www.iaam-online.org), University of Jinan (www.ujn.edu.cn),Journal of Inorganic and Organometallic Polymers and Materials, Springer (www.springerlink.com/content/1574-1443/20/3) and the IAAMs official journal Advanced Materials Letters (AML, www.amlett.com) to be held from 7-9th May, 2011 at the University of Jinan, Jinan, China (www.ujn.edu.cn). The goal of the 1st AM-2011 congress is to focus on major developments in the rapidly expanding field of Advanced Materials and Engineering. Each session will focus on specific aspects of Advanced Materials. The full manuscripts of all major presentations in all sessions will be published after peer review in the special issues of Journal of Inorganic and Organometallic Polymers and Materials, Springer (www.springerlink.com/content/1574-1443/20/3) and the IAAMs official journal Advanced Materials Letters (www.amlett.com). For the computational session you are invited to submit abstracts that may satisfy any of the three categories below: 1. Plenary speaker 2. Key note Lecture 3. Oral presentation Look forward to hearing from you. Kind regards and Best wishes, Ms. Penny P. Govender (pennyg\a/uj.ac.za) Member, International Organizing committee (Computational Chemistry), Advanced Materials Congress- 2011; 7-9 May, 2011 University of Jinan, Jinan, China, http://www.ujn.edu.cn/english/index.php From owner-chemistry@ccl.net Tue Oct 5 07:03:00 2010 From: "klamt],[cosmologic.de" To: CCL Subject: CCL: Experimental Solvation free energy Message-Id: <-42901-101005064852-19935-D7zuo+GS+2jQeIZKLozYSQ+/-server.ccl.net> X-Original-From: klamt]![cosmologic.de Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 05 Oct 2010 12:48:42 +0200 MIME-Version: 1.0 Sent to CCL by: klamt|-|cosmologic.de Hi William, first of all, I guess you want dG_hydr, i.e. solvent beig water. Since it also was not in the 2343 dG_solv data set which was collected by Cramer and Truhlar for their SM8 fitting, I guess that there is no published data available. If you should be interested in the COSMOtherm prediction: dG_hydr(iodobenzene) = -2.30 kcal/mol (reference system: 1 mol/l in gasphase and solvent). Andreas Am 04.10.2010 22:28, schrieb W Flak williamflak::yahoo.com: > Sent to CCL by: "W Flak" [williamflak*|*yahoo.com] > Dear CCL > It may be not the right place to post my question, so I'd like to apologize > firstly for that. I have been searching for the experimental value of the solvation free energy of iodobenzene, but I couldn't find it. I used crossfire > software, and many other databases. > So, I was wondering if you know where I can find this experimental value, > please. > Thanks in advance > W. Flak From owner-chemistry@ccl.net Tue Oct 5 07:49:00 2010 From: "Osama T Akoubeh dolkeen _ hotmail.com" To: CCL Subject: CCL: AsMe3 Computing and correction enthalpy Message-Id: <-42902-101005074702-31853-SvwO3v9EYYlNm2dkATHRnw],[server.ccl.net> X-Original-From: "Osama T Akoubeh" Date: Tue, 5 Oct 2010 07:47:01 -0400 Sent to CCL by: "Osama T Akoubeh" [dolkeen__hotmail.com] The enthalpy result from chemkin is 2929.537 and from leterature 2800 kcal/mol , is it possible chemically to correct the value by multiplying with a factor : The factor : 2800/2929.537 = 0.955782 to obtain a the corrected one and to multiply each thermodynamic properties such as Cp , S and H with this factor , so I can prepare a new Chemkin polynomial with corrcted one anyone can help to see if this procedure correct Osama From owner-chemistry@ccl.net Tue Oct 5 10:23:00 2010 From: "bobby sitayya{:}gmail.com" To: CCL Subject: CCL:G: G03 checkpoint file of ONIOM Message-Id: <-42903-101004082739-15517-jShlJeYtnjKXGtLCg6zBpQ]|[server.ccl.net> X-Original-From: bobby Content-Type: multipart/alternative; boundary=000e0cd1e3081ee9130491c9abe7 Date: Mon, 4 Oct 2010 08:27:31 -0400 MIME-Version: 1.0 Sent to CCL by: bobby [sitayya%x%gmail.com] --000e0cd1e3081ee9130491c9abe7 Content-Type: text/plain; charset=ISO-8859-1 Dear, You need to increase the default GAUSS_MEMDEF size for formatting the checkpoint of ONIOM file if you are on linux/max you should change the GAUSS_MEMDEF environment variable (ex. if you are in C shell, you should use setenv GAUSS_MEMDEFF 4000MB ) That should solve the problem. If not give more details of what you did and your output file. On Mon, Oct 4, 2010 at 5:46 AM, Miko Felix mfx=mmqc.org < owner-chemistry:ccl.net> wrote: > > Sent to CCL by: "Miko Felix" [mfx(-)mmqc.org] > Dear CCLers, > > has anyone ever tried to get the formatted checkpoint file in G03 out of > the > ONIOM calculation? The following command: > > GAUSS_MEMDEF=9000000 formchk pro-ext-recalc.gjf.chk > pro-ext-recalc.gjf.fchk > > gives in the output only MM-part. (GAUSS_MEMDEF is required, otherwise > formchk will segfault) > > The header then looks like this: > > .. > FOpt ONIOM(B3LYP/6-31G(d):AMBER/ZDO) Mixed > Number of atoms I 2048 > Charge I 0 > Multiplicity I 2 > Number of electrons I 0 > Number of alpha electrons I 0 > Number of beta electrons I 0 > Number of basis functions I 0 > Number of independant functions I 0 > Number of point charges in /Mol/ I 0 > Number of translation vectors I 0 > > How do I get the formatted checkpoint file with the QM-region inside? I > could not find any information nor hints in Gaussian manual. > > Thanks, MFX> > > --000e0cd1e3081ee9130491c9abe7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear,
You need to increase the default GAUSS_MEMDEF size for formatting= the checkpoint of ONIOM file
if you are on linux/max you should change = the GAUSS_MEMDEF environment variable (ex. if you are in C shell, you shoul= d use
setenv GAUSS_MEMDEFF 4000MB )

That should solve the problem.
If = not give more details of what you did and your output file.



=


On Mon, Oct 4, 2010 at 5:46 AM, Miko= Felix mfx=3Dmmqc.org <= ;owner-chemistry:ccl.net>= wrote:

Sent to CCL by: "Miko =A0Felix" [mfx(-)mmqc.org]
=A0Dear CCLers,

=A0has anyone ever tried to get the formatted checkpoint file in G03 out of= the
ONIOM calculation? The following command:

=A0GAUSS_MEMDEF=3D9000000 formchk pro-ext-recalc.gjf.chk pro-ext-recalc.gjf= .fchk

gives in the output only MM-part. (GAUSS_MEMDEF is required, otherwise
formchk will segfault)

The header then looks like this:

..
FOpt =A0 =A0 =A0ONIOM(B3LYP/6-31G(d):AMBER/ZDO) =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0 Mixed
Number of atoms =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0I = =A0 =A0 =A0 =A0 =A0 =A0 2048
Charge =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 I =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00
Multiplicity =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 I = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02
Number of electrons =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0I =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A00
Number of alpha electrons =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0I =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A00
Number of beta electrons =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 I =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A00
Number of basis functions =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0I =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A00
Number of independant functions =A0 =A0 =A0 =A0 =A0 =A0I =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A00
Number of point charges in /Mol/ =A0 =A0 =A0 =A0 =A0 I =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A00
Number of translation vectors =A0 =A0 =A0 =A0 =A0 =A0 =A0I =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A00

How do I get the formatted checkpoint file with the QM-region inside? I
could not find any information nor hints in Gaussian manual.

=A0Thanks, MFX



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--000e0cd1e3081ee9130491c9abe7-- From owner-chemistry@ccl.net Tue Oct 5 13:27:00 2010 From: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?= reynier.suardiaz=gmail.com" To: CCL Subject: CCL:G: freezen dihedrals in five-membered rings Message-Id: <-42904-101005131105-23581-JU47sYTc63iuPXMcFSVQEw**server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?= Content-Type: multipart/alternative; boundary=0016364d2989932fa30491e1bddf Date: Tue, 5 Oct 2010 19:10:40 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?= [reynier.suardiaz%a%gmail.com] --0016364d2989932fa30491e1bddf Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Patrick Thanks for the reference. I have downloaded the article and it has been ver= y enlightening. Anyway I would like to reformulate the question or doing another new in a very simple form. * Does anybody knows a software capable of generating many conformations (hundreds) of five-membered rings not only main conformers? If this conformations can be generated from pseudorotation parameters would be grea= t but it is not indispensable.* I would use this geometries to later perform partial optimizations in Gaussian. many thanks in advance Reynier 2010/9/28 Patrick McCarren patrick.mccarren]|[gmail.com < owner-chemistry::ccl.net> > I don't have access to this paper but you might find some details or > contact for obtaining a program for accomplishing this in the paper below= . > > http://scripts.iucr.org/cgi-bin/paper?pn0051 > Constructing rings of specified puckerR. P. Millaneand E. > U. Nzewi > > *Abstract:* A method of constructing closed rings of specified pucker is > described. A ring is constructed such that a set of puckering parameters = as > well as the ring bond lengths and bond angles are optimized towards desir= ed > values. A computer program is described which generates *N*-membered ring= s > in this way and is illustrated with examples. > > Patrick > > > On Tue, Sep 28, 2010 at 8:54 AM, Reynier Suardiaz del R=EDo > reynier.suardiaz(a)gmail.com > > wrote: > >> Dear Patrick >> Thanks a lot for your answer. The idea of using the main conformers soun= d >> very well but what I really would like to do is, besides those conformer= s, >> generate much more at intermediate positions. What is really happening i= s >> that I thought if I change the dihedrals in Gaussian using redundant >> coordinates, the software would change all dihedrals (without problems >> because the combinations of dihedrals should be permitted) and performe = a >> partial optimization in this new conformation. After that, I would write >> some simple code to automatically change the dihedrals to many permitted >> values (to do that, I need the mathematical relation between dihedrals) = and >> to obtain many partially optimized conformations that I could use to >> calculate properties. That plan does not work.... :-( 1st Gaussian can o= nly >> perform the partial optimization if you freeze the dihedrals at the same >> value of the input geometry, if you change this values even to other >> geometrically permitted combinations of dihedrals the calculations ends >> abnormally. 2nd I do not have the mathematical relation between the >> dihedrals in order to change one of them and predict the permitted value= s of >> the others. So I could try to "play" with the geometries trying to find >> suitable combinations in some way as suggested by Pierre or David (many >> thanks to both) or I can look for a code to generate many conformers of = a >> five membered ring as PUCKER mentioned by David Pensak (thanks a lot, I,= ve >> been trying to find this code unsuccessfully). I am sure there is other >> codes that can deal with those conformations of five-membered ring and >> generate a lot of them. Maybe I should formulate a different question to= CCL >> asking for this software (preferably free) >> All the best >> Reynier >> >> >> 2010/9/25 Patrick McCarren patrick.mccarren],[gmail.com > ~~ ccl.net > >> >>> It sounds like the constraints are conflicting but the errors are not a= s >>> helpful as the input would be. Maybe you could provide your input file= ? I >>> think this will be difficult to do using Gaussian alone. I would perso= nally >>> recommend just making each of the 20 fundamental ring conformers (E1, E= 2, >>> E3, E4, E5, 1E, 2E, 3E, 4E, 5E, 1T2, 2T1, etc. ) in a builder program, = do a >>> modredundant optimization with "D * * * * F" to fix all dihedrals at fi= rst, >>> and then do an unfrozen optimization. You might have to gradually remo= ve >>> restraints so you don't lose higher energy ring conformations if that's= what >>> you're trying to do. Another thing you could try is to use a conformat= ional >>> search program with a ring-sampling algorithm. Spartan, MacroModel, MO= E are >>> a couple examples. You could put those structures in Gaussian, constra= in >>> the ring dihedrals as above, optimize, and then reoptimize without >>> constraints. It depends on what you're trying to figure out though. >>> >>> Patrick >>> >>> >>> On Fri, Sep 24, 2010 at 3:27 PM, Reynier Suardiaz del R=EDo >>> reynier.suardiaz!^!gmail.com >>> > wrote: >>> >>>> Dear D. Close >>>> >>>> Many thanks for your answer, you was right. I typed the values of the >>>> dihedrals with 6 decimal places exactly matching with those of the inp= ut >>>> structure. Doing this, the geometry optimization have finished without >>>> problem in a few iterations. Now what I would like to do is the follow= ing: I >>>> want to generate diferent conformations of this furanose ring by chang= ing >>>> the dihedrals (between permitted values without breaking of the ring) = and >>>> partially optimize this structures (obtained by slightly changing the >>>> dihedral values) and keeping frozen the five dihedrals. When I try to = do >>>> this using redundant coordinates in gaussian I obtained the same error >>>> message than before: >>>> >>>> ------------- >>>> Iteration 99 RMS(Cart)=3D 0.00005822 RMS(Int)=3D 0.00955580 >>>> Iteration100 RMS(Cart)=3D 0.00005748 RMS(Int)=3D 0.00959825 >>>> New curvilinear step not converged. >>>> Error imposing constraints >>>> Error termination via Lnk1e in C:\G03W\l101.exe at Fri Sep 24 21:05:0= 6 >>>> 2010. >>>> Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. >>>> File lengths (MBytes): RWF=3D 7 Int=3D 0 D2E=3D 0 Chk= =3D 8 >>>> Scr=3D 1 >>>> -------------- >>>> >>>> even if I only change one dihedral from its original value (at the inp= ut >>>> geometry) in less than one degree, the calculation ends with the abov= e >>>> error message. >>>> Does anybody knows how to do this in gaussian, I mean, changing the >>>> dihedral angles of a five memebered ring (from its text input file) an= d to >>>> performe a partial geometrical optimization with diferent dihedral ang= les, >>>> other than the one of the input geometry? >>>> any comment or suggestions are welcome. >>>> >>>> thanks in advance and with very best regards >>>> >>>> Reynier >>>> >>>> >>>> 2010/9/22 Close, David M. CLOSED~!~mail.etsu.edu < >>>> owner-chemistry]*[ccl.net> >>>> >>>>> >>>>> Sent to CCL by: "Close, David M." [CLOSED#,#mail.etsu.edu] >>>>> Reynier: >>>>> There is no limit to how many dihedrals you can freeze. The problem >>>>> is that you typed something wrong. Notice that the program tried 99 >>>>> iterations to fit you frozen coordiate information into the optimizat= ion >>>>> routine. >>>>> Either you connected the coordinates incorrectly, or did not have >>>>> enough precision in the frozen coordinate. >>>>> So if the input line has something like 10 5 6 8 31.3, first look a= t >>>>> the string 10 5 6 8 and make sure this is correct. The use a graphic= s >>>>> program to examine the actual dihedral geometry. Run through the 4 a= toms in >>>>> the string 10 5 6 8 and see what the graphic program thinks the dihed= ral >>>>> angle actually is. Copy the value to 5-6 decimal places and re enter= the >>>>> data. >>>>> If this doesn't work, then you have to use trial and error. You sai= d >>>>> that freezing 2 dihedrals works. But how many iterations did it take= ? I >>>>> would expect only 2-3. If more, then refine the coordinates, and the= n add a >>>>> third frozen dihedral. You can quickly find the offending entry when= the >>>>> optimization routine bombs. >>>>> Regards, Dave Close. >>>>> >>>>> ________________________________________ >>>>> > From: owner-chemistry+closed=3D=3Detsu.edu[A]ccl.net[owner-chemistr= y+closed=3D=3D >>>>> etsu.edu[A]ccl.net] on behalf of Reynier Suard az reynier.suardiaz(a) >>>>> gmail.com [owner-chemistry[A]ccl.net] >>>>> Sent: Wednesday, September 22, 2010 10:49 AM >>>>> To: Close, David M. >>>>> Subject: CCL:G: freezen dihedrals in five-membered rings >>>>> >>>>> Sent to CCL by: "Reynier Suard az" [reynier.suardiaz]_[gmail.com] >>>>> Dear All >>>>> >>>>> I want to generate a lot of conformations of furanose ring (or >>>>> cyclopentane?) and later partially optimize them but keeping frozen t= he >>>>> dihedral angles. I am trying to use redundant coordinates in gaussian >>>>> writing at the end of the input gaussian file the desired dihedrals t= o keep >>>>> frozen. I am receiving an error message when i try to keep frozen mor= e than >>>>> two dihedral angles (of the ring) at the same time. For example if I = try to >>>>> froze the five dihedrals of the ring I get the following message: >>>>> >>>>> ------ >>>>> Iteration 99 RMS(Cart)=3D 0.00001156 RMS(Int)=3D 0.00309967 >>>>> Iteration100 RMS(Cart)=3D 0.00001134 RMS(Int)=3D 0.00310385 >>>>> New curvilinear step not converged. >>>>> Error imposing constraints >>>>> Error termination via Lnk1e in C:\G03W\l101.exe at Mon Sep 20 17:48:= 17 >>>>> 2010. >>>>> Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. >>>>> File lengths (MBytes): RWF=3D 7 Int=3D 0 D2E=3D 0 Ch= k=3D >>>>> 7 Scr=3D 1 >>>>> --------- >>>>> >>>>> I receive this error message even when I try to freeze the dihedral a= t >>>>> the same value they already have in the initial structure. >>>>> >>>>> Is not possible what am I trying to do? How can I overcome this probl= em >>>>> with gaussian? Is there any other possibility to do this kind of part= ial >>>>> optimization in five-membered rings? Note that I can not freeze all t= he >>>>> dihedrals using optimization in internal coordinates (opt=3Dz-matrix = with a >>>>> separate input section of "constants") because of to define a z-matri= x of a >>>>> five-membered ring are necesary only two dihedrals, so I have to use >>>>> redundants. >>>>> any comments or sugestions would be appreciatte >>>>> >>>>> thanks in advance and very best regards >>>>> >>>>> Reynierhttp:// >>>>> www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/= sub_unsub.shtmlhttp://www.ccl.net/spammers.txt >>>>> >>>>> >>>>> -=3D This is automatically added to each message by the mailing scrip= t =3D- >>>>> >>>>> E-mail to subscribers: CHEMISTRY]*[ccl.net or use:>>>>> >>>>> E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net or use>>>>> Conferences: >>>>> http://server.ccl.net/chemistry/announcements/conferences/>>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> reynier >>>> http://rincon.uam.es/dir?cw=3D331069946289062 >>>> >>> >>> >> >> >> -- >> reynier >> http://rincon.uam.es/dir?cw=3D331069946289062 >> > > --=20 reynier http://rincon.uam.es/dir?cw=3D331069946289062 --0016364d2989932fa30491e1bddf Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Patrick

Thanks for the reference. I have downloaded the article= and it has been very enlightening. Anyway I would like to reformulate the = question or doing another new in a very simple form.

Does anybody= knows a software capable of generating many conformations (hundreds) of fi= ve-membered rings not only main conformers? If this conformations can be ge= nerated from pseudorotation parameters would be great but it is not indispe= nsable.

I would use this geometries to later perform partial optimizations in G= aussian.

many thanks in advance

Reynier

2010/9/28 Patrick McCarren patrick.mccarren]|[gmail.com <owner-chemistry::ccl.net>
I don't have = access to this paper but you might find some details or contact for obtaini= ng a program for accomplishing this in the paper below.=A0

Constructing rings of specified puck= er

R. P. Millane and E. U. Nzewi

Abstract: A metho= d of constructing closed=20 rings of specified pucker is described. A ring is constructed such that a set of puckering parameters as well as the ring bond lengths and bond=20 angles are optimized towards desired values. A computer program is=20 described which generates N-membered=20 rings in this way and is illustrated with examples.


Patrick


On Tue, Sep 28,= 2010 at 8:54 AM, Reynier Suardiaz del R=EDo reynier.suardiaz(a)gmail.com <owner-chemi= stry!A!ccl.net> wrote:
Dear Patrick
T= hanks a lot for your answer. The idea of using the main conformers sound ve= ry well but what I really would like to do is, besides those conformers, ge= nerate much more at intermediate positions. What is really happening is tha= t I thought if I change the dihedrals in Gaussian using redundant coordinat= es, the software would change all dihedrals (without problems because the c= ombinations of dihedrals should be permitted) and performe a partial optimi= zation in this new conformation. After that, I would write some simple code= to automatically change the dihedrals to many permitted values (to do that= , I need the mathematical relation between dihedrals) and to obtain many pa= rtially optimized conformations that I could use to calculate properties. T= hat plan does not work.... :-( 1st Gaussian can only perform the partial op= timization if you freeze the dihedrals at the same value of the input geome= try, if you change this values even to other geometrically permitted combin= ations of dihedrals the calculations ends abnormally. 2nd I do not have the= mathematical relation between the dihedrals in order to change one of them= and predict the permitted values of the others. So I could try to "pl= ay" with the geometries trying to find suitable combinations in some w= ay as suggested by Pierre or David (many thanks to both) or I can look for = a code to generate many conformers of a five membered ring as PUCKER mentio= ned by David Pensak (thanks a lot, I,ve been trying to find this code unsuc= cessfully). I am sure there is other codes that can deal with those conform= ations of five-membered ring and generate a lot of them. Maybe I should for= mulate a different question to CCL asking for this software (preferably fre= e)
All the best
Reynier


2010/9/25 Patrick McCarren patrick.mccarren]= ,[gmail.com <owner-chemistry ~~ ccl.net>
It sounds like the constraints are conflicting but the errors are not as he= lpful as the input would be.=A0 Maybe you could provide your input file?=A0= I think this will be difficult to do using Gaussian alone.=A0 I would pers= onally recommend just making each of the 20 fundamental ring conformers (E1= , E2, E3, E4, E5, 1E, 2E, 3E, 4E, 5E, 1T2, 2T1, etc. ) in a builder program= , do a modredundant optimization with "D * * * * F" to fix all di= hedrals at first, and then do an unfrozen optimization.=A0 You might have t= o gradually remove restraints so you don't lose higher energy ring conf= ormations if that's what you're trying to do.=A0 Another thing you = could try is to use a conformational search program with a ring-sampling al= gorithm.=A0 Spartan, MacroModel, MOE are a couple examples.=A0 You could pu= t those structures in Gaussian, constrain the ring dihedrals as above, opti= mize, and then reoptimize without constraints.=A0 It depends on what you= 9;re trying to figure out though.=A0

Patrick


On Fri, = Sep 24, 2010 at 3:27 PM, Reynier Suardiaz del R=EDo reynier.suardiaz!^!gmail.com = <owner-= chemistry ~ ccl.net> wrote:
Dear D. Close
=
Many thanks for your answer, you was right. I typed the values of the d= ihedrals with 6 decimal places exactly matching with those of the input str= ucture. Doing this, the geometry optimization have finished without problem= in a few iterations. Now what I would like to do is the following: I want = to generate diferent conformations of this furanose ring by changing the di= hedrals (between permitted values without breaking of the ring) and partial= ly optimize this structures (obtained by slightly changing the dihedral val= ues) and keeping frozen the five dihedrals. When I try to do this using red= undant coordinates in gaussian I obtained the same error message than befor= e:

-------------
=A0Iteration 99 RMS(Cart)=3D=A0 0.00005822 RMS(Int)=3D= =A0 0.00955580
=A0Iteration100 RMS(Cart)=3D=A0 0.00005748 RMS(Int)=3D=A0= 0.00959825
=A0New curvilinear step not converged.
=A0Error imposing = constraints
=A0Error termination via Lnk1e in C:\G03W\l101.exe at Fri Se= p 24 21:05:06 2010.
=A0Job cpu time:=A0 0 days=A0 0 hours=A0 0 minutes=A0 1.0 seconds.
=A0Fi= le lengths (MBytes):=A0 RWF=3D=A0=A0=A0=A0=A0 7 Int=3D=A0=A0=A0=A0=A0 0 D2E= =3D=A0=A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 8 Scr=3D=A0=A0=A0=A0=A0 1
---= -----------

even if I only change one dihedral from its original val= ue (at the input geometry) in less than one degree,=A0 the calculation ends= with the above error message.
Does anybody knows how to do this in gaussian, I mean, changing the dihedra= l angles of a five memebered ring (from its text input file) and to perform= e a partial geometrical optimization with diferent dihedral angles, other t= han the one of the input geometry?
any comment or suggestions are welcome.

thanks in advance and with v= ery best regards

Reynier


2010/= 9/22 Close, David M. CLOSED~!~mail.etsu.edu <owner-chemistry]*[ccl.net><= br>

Sent to CCL by: "Close, David M." [CLOSED#,#mail.etsu.edu]
Reynier:
=A0There is no limit to how many dihedrals you can freeze. =A0The problem = is that you typed something wrong. =A0Notice that the program tried 99 iter= ations to fit you frozen coordiate information into the optimization routin= e.
Either you connected the coordinates incorrectly, or did not have enough pr= ecision in the frozen coordinate.
So if the input line has something like 10 5 6 8 =A0 31.3, first look at th= e string 10 5 6 8 and make sure this is correct. =A0The use a graphics prog= ram to examine the actual dihedral geometry. =A0Run through the 4 atoms in = the string 10 5 6 8 and see what the graphic program thinks the dihedral an= gle actually is. =A0Copy the value to 5-6 decimal places and re enter the d= ata.
=A0If this doesn't work, then you have to use trial and error. =A0You = said that freezing 2 dihedrals works. =A0But how many iterations did it tak= e? =A0I would expect only 2-3. =A0If more, then refine the coordinates, and= then add a third frozen dihedral. =A0You can quickly find the offending en= try when the optimization routine bombs.
=A0Regards, Dave Close.

________________________________________
> From: owner-chemistry+closed=3D=3Detsu.edu[A]ccl= .net [owner-chemistry+closed=3D=3Detsu.edu[A]ccl.ne= t] on behalf of Reynier Suard az reynier.suardiaz(a)gmail.com [owner-chemistry[A]ccl.net]
Sent: Wednesday, September 22, 2010 10:49 AM
To: Close, David M.
Subject: CCL:G: freezen dihedrals in five-membered rings

Sent to CCL by: "Reynier =A0Suard =A0az" [reynier.suardiaz]_[gmail.com]
Dear All

I want to generate a lot of conformations of furanose ring (or cyclopentane= ?) and later partially optimize them but keeping frozen the dihedral angles= . I am trying to use redundant coordinates in gaussian writing at the end o= f the input gaussian file the desired dihedrals to keep frozen. I am receiv= ing an error message when i try to keep frozen more than two dihedral angle= s (of the ring) at the same time. For example if I try to froze the five di= hedrals of the ring I get the following message:

------
=A0Iteration 99 RMS(Cart)=3D =A00.00001156 RMS(Int)=3D =A00.00309967
=A0Iteration100 RMS(Cart)=3D =A00.00001134 RMS(Int)=3D =A00.00310385
=A0New curvilinear step not converged.
=A0Error imposing constraints
=A0Error termination via Lnk1e in C:\G03W\l101.exe at Mon Sep 20 17:48:17 2= 010.
=A0Job cpu time: =A00 days =A00 hours =A00 minutes =A01.0 seconds.
=A0File lengths (MBytes): =A0RWF=3D =A0 =A0 =A07 Int=3D =A0 =A0 =A00 D2E=3D= =A0 =A0 =A00 Chk=3D =A0 =A0 =A07 Scr=3D =A0 =A0 =A01
---------

I receive this error message even when I try to freeze the dihedral at the = same value they already have in the initial structure.

Is not possible what am I trying to do? How can I overcome this problem wit= h gaussian? Is there any other possibility to do this kind of partial optim= ization in five-membered rings? Note that I can not freeze all the dihedral= s using optimization in internal coordinates (opt=3Dz-matrix with a separat= e input section of "constants") because of to define a z-matrix o= f a five-membered ring are necesary only two dihedrals, so I have to use re= dundants.
any comments or sugestions would be appreciatte

thanks in advance and very best regards

Reynierhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.c= cl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt



--
reynier
= http://rincon.uam.es/dir?cw=3D331069946289062




--
reynier
= http://rincon.uam.es/dir?cw=3D331069946289062




--
reynier
= http://rincon.uam= .es/dir?cw=3D331069946289062
--0016364d2989932fa30491e1bddf-- From owner-chemistry@ccl.net Tue Oct 5 14:02:00 2010 From: "Bilel Mansouri bilelmansouri80*o*yahoo.fr" To: CCL Subject: CCL:G: help Message-Id: <-42905-101005103318-5119-cGGj1xLM/NMeE68txuzLNg * server.ccl.net> X-Original-From: Bilel Mansouri Content-Type: multipart/alternative; boundary="0-1288656259-1286289192=:15791" Date: Tue, 5 Oct 2010 14:33:12 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Bilel Mansouri [bilelmansouri80^^^yahoo.fr] --0-1288656259-1286289192=:15791 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable > Hi --=0A=0A> I'm doing a (what I thought was simple) test job of=A0tow=A0= water molecules whith =0A>supermolecule methode=A0using B3LYP=0A> and the 6= -311G basis set.=0AI have the error message =0ANo NMR shielding tensors so = no spin-rotation constants.=0A=A0Leave Link=A0 601 at Wed Oct 06 15:29:37 2= 010, MaxMem=3D=A0=A0=A0 6291456 cpu:=A0=A0=A0=A0=A0=A0 0.0=0A=A0(Enter C:\G= 03W\l9999.exe)=0A=0A=A0What some people mistake for the high cost=0A=A0of l= iving is really the cost of living high.=0A=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -- Doug Larson=0A= =A0Error termination request processed by link 9999.=0A=A0Error termination= via Lnk1e in C:\G03W\l9999.exe at Wed Oct 06 15:29:37 2010.=0A=A0Job cpu t= ime:=A0 0 days=A0 0 hours 13 minutes 33.0 seconds.=0A=A0File lengths (MByte= s):=A0 RWF=3D=A0=A0=A0=A0 11 Int=3D=A0=A0=A0=A0=A0 0 D2E=3D=A0=A0=A0=A0=A0 = 0 Chk=3D=A0=A0=A0=A0=A0 8 =0AScr=3D=A0=A0=A0=A0=A0 1=0A=0A=A0Any insight wo= uld be very helpful.=0A=0A=0A=A0Thanks!=0A=0A=0A=0A --0-1288656259-1286289192=:15791 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
> Hi --

> I'm doing a (what I thought was= simple) test job of tow water molecules whith supermolecule meth= ode using B3LYP
> and the 6-311G basis set.
I have the error = message
=0A
No NMR shielding tensors so no spin-rotation constant= s.
 Leave Link  601 at Wed Oct 06 15:29:37 2010, MaxMem=3D&nbs= p;   6291456 cpu:       0.0
&nbs= p;(Enter C:\G03W\l9999.exe)
=0A

 What some people mistake= for the high cost
 of living is really the cost of living high.            &n= bsp;            = ;     -- Doug Larson
 Error termination request= processed by link 9999.
 Error termination via Lnk1e in C:\G03W\l9= 999.exe at Wed Oct 06 15:29:37 2010.
 Job cpu time:  0 days&nb= sp; 0 hours 13 minutes 33.0 seconds.
 File lengths (MBytes):  = RWF=3D     11 Int=3D      0 D2= E=3D      0 Chk=3D      8= Scr=3D      1
=0A
 Any insight = would be very helpful.

=0A
 Thanks!
=0A=0A=0A=0A=0A --0-1288656259-1286289192=:15791-- From owner-chemistry@ccl.net Tue Oct 5 14:37:00 2010 From: "Rene Thomsen rt---molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Virtual Docker 4.2 Message-Id: <-42906-101005131656-7165-EmlQljclorNDOsyaeQrt3A]=[server.ccl.net> X-Original-From: "Rene Thomsen" Date: Tue, 5 Oct 2010 13:16:54 -0400 Sent to CCL by: "Rene Thomsen" [rt=molegro.com] Aarhus, Denmark, October 4th, 2010 - Molegro is pleased to announce a new release of Molegro Virtual Docker, an integrated platform for computational drug design available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality protein-ligand docking based on novel optimization techniques combined with a user interface experience focusing on usability and productivity. New features in version 4.2: * Support for custom coloring of molecules (atoms, residues, rings). * Visualization of hydrogen bonds and electrostatic interactions can now be customized. * Visualization settings (e.g. graphic styles, camera settings, custom coloring) is now stored in the workspace file (MVDML). * PDB header information and SDF annotations are now imported and stored as part of the workspace. * Improved parsing of PDB files (e.g. using PDB Compliancy information if available and refined thresholds for detecting covalent bonds). * Minor user interface improvements and bug fixes. For more information, or to download a trial version, please visit our company website at: http://www.molegro.com or contact: Rene Thomsen, CEO Molegro C. F. Moellers Alle 8, Bldg. 1110 DK-8000 Aarhus Denmark E-mail: rt#%#molegro.com Phone: (+45) 89 42 31 65 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high- performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Tue Oct 5 15:28:00 2010 From: "Kalju Kahn kalju+/-chem.ucsb.edu" To: CCL Subject: CCL: AsMe3 Computing and correction enthalpy Message-Id: <-42907-101005150225-13865-zAdjEACBTo0V+PcSlIc/vw]^[server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 5 Oct 2010 12:01:46 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju/a\chem.ucsb.edu] Osama, Your proposed correction is not valid, in general entropy and enthalpy are two different things and you should not expect that their errors are (linearly) correlated. Calculated errors in H and S may be correlated. For example, a computational method that underestimates the enthalpy of binding of two monomers in a bimolecular complex will likely predict that the the vibrational entropy due to the vibration along the complex dissociation mode is too high (the complex is calculated to be too loose). But the relationship is complex enough that you can't use the known enthalpy error to correct the entropy value. Sometime, calculated errors in H and S have the same source. An example of this is the vibrational correction for H(thermal) and S. It is well known that Hartree-Fock method overestimates harmonic bond stretching frequencies by ca 10%. Thus it is justified to scale frequencies, and use scaled frequencies to calculate better H(thermal) and S. But in your case, it is the H(electronic) that is wrong. /sarcasm To get the correct Cp, multiply your calculated result by Tambov constant, to get the correct S, divide your number by Skinner constant if this fails develop your own density functional that will reproduce the experimentally observed values. end sarcasm/ Kalju > > Sent to CCL by: "Osama T Akoubeh" [dolkeen__hotmail.com] > > The enthalpy result from chemkin is 2929.537 and from leterature 2800 > kcal/mol , is it possible chemically to correct the value by multiplying > with a factor : The factor : 2800/2929.537 = 0.955782 to obtain a the > corrected one and to multiply each thermodynamic properties such as Cp , S > and H with this factor , so I can prepare a new Chemkin polynomial with > corrcted one > > anyone can help to see if this procedure correct > > Osama ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Tue Oct 5 18:26:00 2010 From: "William Flak williamflak.*_*.yahoo.com" To: CCL Subject: CCL: Experimental Solvation free energy Message-Id: <-42908-101005181809-15566-kRyqbnSY3xwllk9zW4ndpQ*_*server.ccl.net> X-Original-From: William Flak Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 5 Oct 2010 15:18:03 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: William Flak [williamflak],[yahoo.com] Dear Prof Andreas Thanks so much for you reply. My calculation shows that dG(hyd) of Iodobenzene = -1.79 kcalmol So, I was wondering what level of calculation did you use to get -2.3, and which software. In addition, where can I find this Cramer database for 2343 molecule? Thanks in advance W. Flak --- On Tue, 10/5/10, klamt],[cosmologic.de wrote: > From: klamt],[cosmologic.de > Subject: CCL: Experimental Solvation free energy > To: "Flak, William " > Date: Tuesday, October 5, 2010, 10:48 AM > > Sent to CCL by: klamt|-|cosmologic.de > Hi William, > > first of all, I guess you want dG_hydr, i.e. solvent beig > water. > Since it also was not in the 2343 dG_solv data set which > was collected by Cramer > and Truhlar for their SM8 fitting, I guess that there is no > published data > available. > If you should be interested in the COSMOtherm prediction: > dG_hydr(iodobenzene) = > -2.30 kcal/mol (reference system: 1 mol/l in gasphase and > solvent). > > Andreas > > > Am 04.10.2010 22:28, schrieb W Flak > williamflak::yahoo.com: > > Sent to CCL by: "W  Flak" > [williamflak*|*yahoo.com] > > Dear CCL > > It may be not the right place to post my question, so > I'd like to apologize > > firstly for that. I have been searching for the > experimental value of the > solvation free energy of iodobenzene, but I couldn't find > it. I used crossfire > > software, and many other databases. > > So, I was wondering if you know where I can find this > experimental value, > > please. > > Thanks in advance > > W. Flak > > > > -= This is automatically added to each message by the > mailing script =- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the _._ sign. You > can also> > E-mail to subscribers: CHEMISTRY_._ccl.net > or use: >      > > E-mail to administrators: CHEMISTRY-REQUEST_._ccl.net > or use >      >      >      > > > From owner-chemistry@ccl.net Tue Oct 5 21:39:00 2010 From: "Jamin Krinsky jamink%a%berkeley.edu" To: CCL Subject: CCL:G: help Message-Id: <-42909-101005155015-13218-Pw2N6q4E+lZQRme0ftyf7w ~ server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 5 Oct 2010 12:49:57 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink[]berkeley.edu] Hi Bilel, I'm not sure I understand what type of calculation you are doing, but the message: "No NMR shielding tensors so no spin-rotation constants" is not really an error message, and the fact that you got a quote suggests that the calculation finished correctly. Also, it ran 13 minutes and you only have two water molecules... The error is in link 9999, not link 601 where you got that message. Link 9999 is the final close-down-the-job link so most of the time an error in this part means it cannot do archiving or something. It would help if you included your actual input in your post, as there might be an obvious keyword incompatibility or something. Jamin On Tue, Oct 5, 2010 at 7:33 AM, Bilel Mansouri bilelmansouri80*o*yahoo.fr wrote: >> Hi -- > >> I'm doing a (what I thought was simple) test job of tow water molecules >> whith supermolecule methode using B3LYP >> and the 6-311G basis set. > I have the error message > No NMR shielding tensors so no spin-rotation constants. >  Leave Link  601 at Wed Oct 06 15:29:37 2010, MaxMem=    6291456 cpu: > 0.0 >  (Enter C:\G03W\l9999.exe) >  What some people mistake for the high cost >  of living is really the cost of living high. >                               -- Doug Larson >  Error termination request processed by link 9999. >  Error termination via Lnk1e in C:\G03W\l9999.exe at Wed Oct 06 15:29:37 > 2010. >  Job cpu time:  0 days  0 hours 13 minutes 33.0 seconds. >  File lengths (MBytes):  RWF=     11 Int=      0 D2E=      0 Chk=      8 > Scr=      1 >  Any insight would be very helpful. > >  Thanks! > >