From owner-chemistry@ccl.net Wed Jul 17 08:30:01 2013 From: "nico green nicogreen6,gmail.com" To: CCL Subject: CCL:G: Finding the transition state Message-Id: <-48967-130717082740-19324-nwXavcn0Io9hV0hHZmHa2w[]server.ccl.net> X-Original-From: nico green Content-Type: multipart/alternative; boundary=001a11c334aad0abf004e1b43776 Date: Wed, 17 Jul 2013 09:27:33 -0300 MIME-Version: 1.0 Sent to CCL by: nico green [nicogreen6%gmail.com] --001a11c334aad0abf004e1b43776 Content-Type: text/plain; charset=ISO-8859-1 I dont remember it the error looke like that on the output, but when i started using the qst2 method i didnt know that i must compare reactants and products and confirm that every atom has the same label in both structures. I always prepare my inputs of qst2 with gaussview and use the mirror view of both structures to check that Hope that helps On 16/07/2013 12:27 PM, "Errol Lewars elewars * trentu.ca" < owner-chemistry.[].ccl.net> wrote: > > Sent to CCL by: Errol Lewars [elewars_+_trentu.ca] > 2013 July 16 > > > "I have not a lot of experience working with theoretical methods, but > something that worked to me in order to find transition structure is use > the berny method (only TS initial guess needed) with the keyword > NoEigenTest, otherwise I found this process very dificult." > > I second that: I have *never* found that (otherwise good) method to work > unless Opt is flagged with NoEigenTest; I suspect the need to add this is > not generally known and is the cause of much trouble finding transition > states. Try an input structure built using simply (?) chemical intuition. > Try ratcheting up a TS from, say, rapid AM1 to the higher desired level . > > E. Lewars > == > > > > > Juan Manuel mayerzmytm#%#gmail.com wrote: > >> Hello Ailar, >> >> I have not a lot of experience working with theoretical methods, but >> something that worked to me in order to find transition structure is use >> the berny method (only TS initial guess needed) with the keyword >> NoEigenTest, otherwise I found this process very dificult >> >> opt=(ts,noeigentest)....... >> >> best >> >> Juan Manuel Arce >> >> >> 2013/7/12 Ailar Badri ailar121242363:-:yahoo.co.uk >> >> >> >> >> >> Sent to CCL by: "Ailar Badri" [ailar121242363-.-yahoo.co.uk >> ] >> Dear CCLers, >> >> I'm looking for transition state structure using qst2 command, but >> I have not been succeed so far. I tried many kinds of >> reactant/product structures to find the transition state. However, >> my calculations always terminate with the following error almost >> immediately after submitting the job: >> >> Old curvilinear step not converged, using linear step: >> SCX= 2.80D+01 DXMaxT= 5.30-317 SCLim= 0.00D+00 Fact= 0.00D+00 >> RedCar/ORedCr failed for GTrans. >> Error termination via Lnk1e in >> /afs/ics.muni.cz/software/g09-**D01/em64t.sse4.2/g09/l101.exe >> > >> at >> Fri Jul 12 15:31:42 2013. >> >> I would be grateful if someone can help me. I am using Gaussian 09 >> rev. D01. >> >> Regards, >> Ailar Badri >> >> >> >> -= This is automatically added to each message by the mailing >> script =- >> 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/ http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --001a11c334aad0abf004e1b43776 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

I dont remember it the error looke=A0 like that on the outpu= t, but when i started using the qst2 method i didnt know that i must compar= e reactants and products and confirm that every atom has the same label in = both structures. I always prepare my inputs of qst2 with gaussview and use = the mirror view of both structures to check that

Hope that helps

On 16/07/2013 12:27 PM, "Errol Lewars elewa= rs * trentu.ca" <owner-chemistry.[].ccl.net> wrote:

Sent to CCL by: Errol Lewars [elewars_+_trentu.ca]
2013 July 16


"I have not a lot of experience working with theoretical methods, but = something that worked to me in order to find transition structure is use th= e berny method (only TS initial guess needed) with the keyword NoEigenTest,= otherwise I found this process very dificult."

I second that: I have *never* found that (otherwise good) method to work un= less Opt is flagged with NoEigenTest; I suspect the need to add this is not= generally known and is the cause of much trouble finding transition states= . Try an input structure built using simply (?) chemical intuition. Try rat= cheting up a TS from, say, rapid AM1 to the higher desired level .

E. Lewars
=3D=3D




Juan Manuel mayerzmytm#%#gma= il.com wrote:
Hello Ailar,

I have not a lot of experience working with theoretical methods, but someth= ing that worked to me in order to find transition structure is use the bern= y method (only TS initial guess needed) with the keyword NoEigenTest, other= wise I found this process very dificult

opt=3D(ts,noeigentest).......

best

Juan Manuel Arce


2013/7/12 Ailar Badri ailar121242363:-:yahoo.co.uk <http://yahoo.co.uk> <owner-chemistry]=3D[ccl.net <mailto:owner-chemistry]=3D[ccl.net>>


=A0 =A0 Sent to CCL by: "Ailar =A0Badri" [ailar121242363-.-yahoo.co.uk
=A0 =A0 <http://yahoo.c= o.uk>]
=A0 =A0 Dear CCLers,

=A0 =A0 I'm looking for transition state structure using qst2 command, = but
=A0 =A0 I have not been succeed so far. I tried many kinds of
=A0 =A0 reactant/product structures to find the transition state. However,<= br> =A0 =A0 my calculations always terminate with the following error almost =A0 =A0 immediately after submitting the job:

=A0 =A0 Old curvilinear step not converged, using linear step:
=A0 =A0 =A0SCX=3D 2.80D+01 DXMaxT=3D 5.30-317 SCLim=3D 0.00D+00 Fact=3D 0.0= 0D+00
=A0 =A0 =A0RedCar/ORedCr failed for GTrans.
=A0 =A0 =A0Error termination via Lnk1e in
=A0 =A0 /afs/ics.muni.cz/software/g09-D01/em64t.sse= 4.2/g09/l101.exe
=A0 =A0 <http://ics.muni.cz/software/g09-D01/em6= 4t.sse4.2/g09/l101.exe> at
=A0 =A0 Fri Jul 12 15:31:42 2013.

=A0 =A0 I would be grateful if someone can help me. I am using Gaussian 09<= br> =A0 =A0 rev. D01.

=A0 =A0 Regards,
=A0 =A0 Ailar Badri



=A0 =A0 -=3D This is automatically added to each message by the mailing
=A0 =A0 script =3D-
=A0 =A0 E-mail to subscribers: CHEMISTRY]=3D[ccl.net
=A0 =A0 <mailto:CHEMISTRY= ]=3D[ccl.net> or us= e:>
=A0 =A0 E-mail to administrators: CHEMISTRY-REQUEST]=3D[ccl.net
=A0 =A0 <mailto:C= HEMISTRY-REQUEST]=3D[cc= l.net> or use> =A0 =A0 Conferences:
=A0 =A0 http://server.ccl.net/chemistry/announcements/= conferences/>





-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY.[].ccl.net or use:
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Before posting, check wait time at: http://www.ccl.net

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--001a11c334aad0abf004e1b43776-- From owner-chemistry@ccl.net Wed Jul 17 21:49:00 2013 From: "Adel Reisi areisi^^^kashanu.ac.ir" To: CCL Subject: CCL:G: question abaut computational chemistry Message-Id: <-48968-130717163628-23017-em5pTxP4vAx7vF19ejgd+A*server.ccl.net> X-Original-From: "Adel Reisi" Date: Wed, 17 Jul 2013 16:36:27 -0400 Sent to CCL by: "Adel Reisi" [areisi_._kashanu.ac.ir] For calculation of rate constants, partition function is necessary, but I doubt what partition function in Gaussian output (Total (Bot)or Total (V=0))must be used? From owner-chemistry@ccl.net Wed Jul 17 22:24:00 2013 From: "Bradley K Welch bwelch5 .. slu.edu" To: CCL Subject: CCL: Generating neighboring molecule Message-Id: <-48969-130717215609-27493-uWXXwRITywkpw4AelX/OCw!A!server.ccl.net> X-Original-From: "Bradley K Welch" Date: Wed, 17 Jul 2013 21:56:08 -0400 Sent to CCL by: "Bradley K Welch" [bwelch5]-[slu.edu] Dear All, I have a .cif of a molecule from the literature. I want to do a calculation on its dimer. The authors give the transformation to generate the neighboring molecule (the .cif does not include the dimer). What software could I use to help me generate the molecule? I have chemcraft and jmol but any other program suggested works would be fine as well. Bradley Welch From owner-chemistry@ccl.net Wed Jul 17 23:53:00 2013 From: "Brad Rose brose::live.com" To: CCL Subject: CCL: Generating neighboring molecule Message-Id: <-48970-130717234436-2055-JKaPts2tStVu+ElWoEvH4A]*[server.ccl.net> X-Original-From: Brad Rose Content-Type: multipart/alternative; boundary="--_com.android.email_566449486994380" Date: Wed, 17 Jul 2013 20:44:18 -0700 MIME-Version: 1.0 Sent to CCL by: Brad Rose [brose,,live.com] ----_com.android.email_566449486994380 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 TWVyY3VyeSBmcm9tIENDREIgaXMgZnJlZSBhbmQgY2FuIGVhc2lseSBkbyB0aGlzIGZyb20gYSBj aWYuCkJyYWQgUm9zZQoKLS0tLS0tLS0gT3JpZ2luYWwgbWVzc2FnZSAtLS0tLS0tLQpGcm9tOiAi QnJhZGxleSBLIFdlbGNoIGJ3ZWxjaDUgLi4gc2x1LmVkdSIgPG93bmVyLWNoZW1pc3RyeUBjY2wu bmV0PiAKRGF0ZTogMDcvMTcvMjAxMyAgNjo1NiBQTSAgKEdNVC0wODowMCkgClRvOiAiUm9zZSwg QnJhZGxleSAtaWQjM2RzLSIgPGJyb3NlQGxpdmUuY29tPiAKU3ViamVjdDogQ0NMOiBHZW5lcmF0 aW5nIG5laWdoYm9yaW5nIG1vbGVjdWxlIAogCgpTZW50IHRvIENDTCBieTogIkJyYWRsZXnCoCBL IFdlbGNoIiBbYndlbGNoNV0tW3NsdS5lZHVdCkRlYXIgQWxsLCAKCkkgaGF2ZSBhIC5jaWYgb2Yg YSBtb2xlY3VsZSBmcm9tIHRoZSBsaXRlcmF0dXJlLiBJIHdhbnQgdG8gZG8gYSBjYWxjdWxhdGlv biBvbiAKaXRzIGRpbWVyLiBUaGUgYXV0aG9ycyBnaXZlIHRoZSB0cmFuc2Zvcm1hdGlvbiB0byBn ZW5lcmF0ZSB0aGUgbmVpZ2hib3JpbmcgCm1vbGVjdWxlICh0aGUgLmNpZiBkb2VzIG5vdCBpbmNs dWRlIHRoZSBkaW1lcikuIFdoYXQgc29mdHdhcmUgY291bGQgSSB1c2UgdG8gCmhlbHAgbWUgZ2Vu ZXJhdGUgdGhlIG1vbGVjdWxlPyBJIGhhdmUgY2hlbWNyYWZ0IGFuZCBqbW9sIGJ1dCBhbnkgb3Ro ZXIgcHJvZ3JhbSAKc3VnZ2VzdGVkIHdvcmtzIHdvdWxkIGJlIGZpbmUgYXMgd2VsbC7CoCAKCkJy YWRsZXkgV2VsY2gKCgoKLT0gVGhpcyBpcyBhdXRvbWF0aWNhbGx5IGFkZGVkIHRvIGVhY2ggbWVz c2FnZSBieSB0aGUgbWFpbGluZyBzY3JpcHQgPS0KVG8gcmVjb3ZlciB0aGUgZW1haWwgYWRkcmVz cyBvZiB0aGUgYXV0aG9yIG9mIHRoZSBtZXNzYWdlLCBwbGVhc2UgY2hhbmdlCnRoZSBzdHJhbmdl IGNoYXJhY3RlcnMgb24gdGhlIHRvcCBsaW5lIHRvIHRoZSBAIHNpZ24uIFlvdSBjYW4gYWxzbwps b29rIHVwIHRoZSBYLU9yaWdpbmFsLUZyb206IGxpbmUgaW4gdGhlIG1haWwgaGVhZGVyLgoKRS1t YWlsIHRvIHN1YnNjcmliZXJzOiBDSEVNSVNUUllAY2NsLm5ldCBvciB1c2U6CsKgwqDCoMKgwqAg aHR0cDovL3d3dy5jY2wubmV0L2NnaS1iaW4vY2NsL3NlbmRfY2NsX21lc3NhZ2UKCkUtbWFpbCB0 byBhZG1pbmlzdHJhdG9yczogQ0hFTUlTVFJZLVJFUVVFU1RAY2NsLm5ldCBvciB1c2UKwqDCoMKg wqDCoCBodHRwOi8vd3d3LmNjbC5uZXQvY2dpLWJpbi9jY2wvc2VuZF9jY2xfbWVzc2FnZQoKU3Vi c2NyaWJlL1Vuc3Vic2NyaWJlOiAKwqDCoMKgwqDCoCBodHRwOi8vd3d3LmNjbC5uZXQvY2hlbWlz dHJ5L3N1Yl91bnN1Yi5zaHRtbAoKQmVmb3JlIHBvc3RpbmcsIGNoZWNrIHdhaXQgdGltZSBhdDog aHR0cDovL3d3dy5jY2wubmV0CgpKb2I6IGh0dHA6Ly93d3cuY2NsLm5ldC9qb2JzIApDb25mZXJl bmNlczogaHR0cDovL3NlcnZlci5jY2wubmV0L2NoZW1pc3RyeS9hbm5vdW5jZW1lbnRzL2NvbmZl cmVuY2VzLwoKU2VhcmNoIE1lc3NhZ2VzOiBodHRwOi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L3Nl YXJjaGNjbC9pbmRleC5zaHRtbAoKSWYgeW91ciBtYWlsIGJvdW5jZXMgZnJvbSBDQ0wgd2l0aCA1 LjcuMSBlcnJvciwgY2hlY2s6CsKgwqDCoMKgwqAgaHR0cDovL3d3dy5jY2wubmV0L3NwYW1tZXJz LnR4dAoKUlRGSTogaHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9hYm91dGNjbC9pbnN0cnVj dGlvbnMvCgoKCg== ----_com.android.email_566449486994380 Content-Type: text/html; 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