From owner-chemistry@ccl.net Tue Mar 8 04:39:00 2011 From: "Lukman Olawale Olasunkanmi waleolasunkanmi|,|gmail.com" To: CCL Subject: CCL: Help on H.O.F. from MOPAC Message-Id: <-44070-110308043444-14474-H4GfxyatwKBbp35/necG+g++server.ccl.net> X-Original-From: "Lukman Olawale Olasunkanmi" Date: Tue, 8 Mar 2011 04:34:42 -0500 Sent to CCL by: "Lukman Olawale Olasunkanmi" [waleolasunkanmi%x%gmail.com] Hello James, Please, what can you say about the reliability of the Heat of Formation (H.O.F) data obtained from MOPAC2009? It seems the values are not well comparable to experimental standard heat of formation values as do S, H and Cp. I also came across a statement: " A new quantity is the heat of formation at the defined T. This is intended for use in calculating heats of reaction. Because of a limitation in the data available, the H.O.F. at T kelvin is defined as "the heat of formation of the compound at T kelvin from its elements in their standard state at 298K". Obviously this definition of H.O.F. is incorrect, but should be useful in calculating heats of reaction, where the elements in their standard states at 298K drop out". Does this statement simply mean that the H.O.F obtained in MOPAC is not quantitatively reliable? Although, I always draw correct qualitative conclusions from the results. More so, any time I specify the keyword THERMO in my calculations, I obtain this warning: "the Gradient is too large for force calculation...", do you think using LET GNORM = 0.01 can solve this problem? Thank you in anticipation of your swift response. From owner-chemistry@ccl.net Tue Mar 8 08:52:00 2011 From: "Cheri McFerrin cmcfer1,+,tigers.lsu.edu" To: CCL Subject: CCL: scan problem Message-Id: <-44071-110308085053-10483-ae/6tO0PX5kVwkFNoljqxg-x-server.ccl.net> X-Original-From: Cheri McFerrin Content-Type: multipart/alternative; boundary=0015177fd00cf4dc92049df8e54e Date: Tue, 8 Mar 2011 07:50:42 -0600 MIME-Version: 1.0 Sent to CCL by: Cheri McFerrin [cmcfer1%a%tigers.lsu.edu] --0015177fd00cf4dc92049df8e54e Content-Type: text/plain; charset=ISO-8859-1 hi zijun you will have to put your coordinates in a z-mat format. afterwards, you may either hold the appropriate angle or dihedral angle constant such that the O doesn't migrate toward the H while you are stretching the O-N bond. be sure to include z-mat in your opt string as well. this is a z-mat for water o h 1 0.98 h 1 0.98 2 109.5 cheri On Mon, Mar 7, 2011 at 6:04 PM, Zijun Yu zjyu-*-lamar.colostate.edu < owner-chemistry:ccl.net> wrote: > > Sent to CCL by: "Zijun Yu" [zjyu.:.lamar.colostate.edu] > Dear All, > I try to do a scan calculation on PETN. Molecular structure is > C(CH2O-NO2)4. I want to scan bond O-N to get NO2 elimination reaction path. > But after 29 steps, the oxygen atom from NO2 forms hydrogen bond with the > hydrogen atom of CH2, and then totally changs the structure to have HONO > elinination. How to scan get the NO2 elimination reaction path? thanks! > > My input file is below: > %chk=ONIOMscan1.chk > %mem=4000MB > %nprocshared=4 > #p oniom(b3lyp/6-31g(d):uff) opt=(modredundant,QuadMacro,maxcycle=300) > scf=(maxcycle=300) nosymm > > scan O26-N27 bond > > 0 1 0 1 0 1 > C-C_3 0 1.42009700 0.53656500 0.25153200 L H-H_ 23 > C-C_3 0 2.07396300 -0.84802900 0.37737100 L > H-H_ 0 1.36956600 -1.56242000 0.80781700 L > H-H_ 0 2.96774300 -0.80139000 1.00252200 L > O-O_R 0 2.42565100 -1.25162100 -0.95419100 L > N-N_R 0 3.01180200 -2.54467800 -1.03268600 L > O-O_R 0 3.15309300 -3.13954200 -0.00064200 L > O-O_R 0 3.28399500 -2.85195300 -2.15091700 L > C-C_3 0 2.44552900 1.51059000 -0.34865100 L > H-H_ 0 3.33484800 1.56157000 0.28248100 L > H-H_ 0 2.73450400 1.20072700 -1.35478600 L > O-O_R 0 1.80541100 2.79425600 -0.39424600 L > N-N_R 0 2.63361700 3.83820100 -0.89022900 L > O-O_R 0 2.07531400 4.89031300 -0.90775200 L > O-O_R 0 3.74807700 3.53753400 -1.21659400 L > C-C_3 0 0.96947700 0.99493300 1.64698200 L > H-H_ 0 0.26948800 0.28048400 2.08450200 L > H-H_ 0 0.49433000 1.97609000 1.58884300 L > O-O_R 0 2.15671100 1.07457400 2.44933100 L > N-N_R 0 1.93014300 1.53029000 3.77701500 L > O-O_R 0 2.93555800 1.59242600 4.41280300 L > O-O_R 0 0.79684600 1.78423000 4.07716600 L > C-C_3 0 0.19136700 0.48882200 -0.66957300 H > H-H_ 0 0.48166000 0.17218300 -1.67320600 H > H-H_ 0 -0.29178400 1.46621100 -0.72530700 H > O-O_R 0 -0.70713000 -0.47190700 -0.09568100 H > N-N_R 0 -1.89509300 -0.67769500 -0.84941300 H > O-O_R 0 -2.01768400 -0.03471500 -1.85464300 H > O-O_R 0 -2.61438000 -1.48554500 -0.35045700 H > > B 26 27 1.42187 S 70 0.05> > > --0015177fd00cf4dc92049df8e54e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable hi zijun

you will have to put your coordinates in a z-ma= t format. =A0afterwards, you may either hold the appropriate angle or dihed= ral angle constant such that the O doesn't migrate toward the H while y= ou are stretching the O-N bond. =A0be sure to include z-mat in your opt str= ing as well.

this is a z-mat for water

o=A0=
h 1 0.98
h 1 0.98 2 109.5

che= ri

On Mon, Mar 7, 2011 at 6:04 PM, Zijun = Yu zjyu-*-lamar.colostate.edu <owner-chemis= try:ccl.net> wrote:

Sent to CCL by: "Zijun =A0Yu" [zjyu.:.lamar.colostate.edu]
Dear All,
I try to do a scan calculation on PETN. Molecular structure is C(CH2O-NO2)4= . I want to scan bond O-N to get NO2 elimination reaction path. But after 2= 9 steps, the oxygen atom from NO2 forms hydrogen bond with the hydrogen ato= m of CH2, and then totally changs the structure to have HONO elinination. H= ow to scan get the NO2 elimination reaction path? thanks!

My input file is below:
%chk=3DONIOMscan1.chk
%mem=3D4000MB
%nprocshared=3D4
#p oniom(b3lyp/6-31g(d):uff) opt=3D(modredundant,QuadMacro,maxcycle=3D300) = scf=3D(maxcycle=3D300) nosymm

scan O26-N27 bond

0 1 0 1 0 1
=A0C-C_3 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.42009700 =A0 =A00.53656500 =A0 = =A00.25153200 L H-H_ 23
=A0C-C_3 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.07396300 =A0 -0.84802900 =A0 =A0= 0.37737100 L
=A0H-H_ =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 =A01.36956600 =A0 -1.56242000 =A0 =A0= 0.80781700 L
=A0H-H_ =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 =A02.96774300 =A0 -0.80139000 =A0 =A0= 1.00252200 L
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.42565100 =A0 -1.25162100 =A0 -0.= 95419100 L
=A0N-N_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A03.01180200 =A0 -2.54467800 =A0 -1.= 03268600 L
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A03.15309300 =A0 -3.13954200 =A0 -0.= 00064200 L
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A03.28399500 =A0 -2.85195300 =A0 -2.= 15091700 L
=A0C-C_3 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.44552900 =A0 =A01.51059000 =A0 -= 0.34865100 L
=A0H-H_ =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 =A03.33484800 =A0 =A01.56157000 =A0 = =A00.28248100 L
=A0H-H_ =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 =A02.73450400 =A0 =A01.20072700 =A0 -= 1.35478600 L
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.80541100 =A0 =A02.79425600 =A0 -= 0.39424600 L
=A0N-N_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.63361700 =A0 =A03.83820100 =A0 -= 0.89022900 L
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.07531400 =A0 =A04.89031300 =A0 -= 0.90775200 L
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A03.74807700 =A0 =A03.53753400 =A0 -= 1.21659400 L
=A0C-C_3 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.96947700 =A0 =A00.99493300 =A0 = =A01.64698200 L
=A0H-H_ =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 =A00.26948800 =A0 =A00.28048400 =A0 = =A02.08450200 L
=A0H-H_ =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 =A00.49433000 =A0 =A01.97609000 =A0 = =A01.58884300 L
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.15671100 =A0 =A01.07457400 =A0 = =A02.44933100 L
=A0N-N_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.93014300 =A0 =A01.53029000 =A0 = =A03.77701500 L
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.93555800 =A0 =A01.59242600 =A0 = =A04.41280300 L
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.79684600 =A0 =A01.78423000 =A0 = =A04.07716600 L
=A0C-C_3 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.19136700 =A0 =A00.48882200 =A0 -= 0.66957300 H
=A0H-H_ =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 =A00.48166000 =A0 =A00.17218300 =A0 -= 1.67320600 H
=A0H-H_ =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 -0.29178400 =A0 =A01.46621100 =A0 -0.= 72530700 H
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 -0.70713000 =A0 -0.47190700 =A0 -0.09= 568100 H
=A0N-N_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 -1.89509300 =A0 -0.67769500 =A0 -0.84= 941300 H
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.01768400 =A0 -0.03471500 =A0 -1.85= 464300 H
=A0O-O_R =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.61438000 =A0 -1.48554500 =A0 -0.35= 045700 H

B 26 27 1.42187 S 70 0.05



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--0015177fd00cf4dc92049df8e54e-- From owner-chemistry@ccl.net Tue Mar 8 10:43:00 2011 From: "Jimmy Stewart MrMOPAC!=!att.net" To: CCL Subject: CCL: Help on H.O.F. from MOPAC Message-Id: <-44072-110308104119-10370-kOzC4J0BcAaMiIYkXvMrLA . server.ccl.net> X-Original-From: Jimmy Stewart Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Tue, 08 Mar 2011 08:40:52 -0700 Mime-Version: 1.0 Sent to CCL by: Jimmy Stewart [MrMOPAC~~att.net] Dr Olasunkanmi asked about the accuracy of the methods in MOPAC. There are tables and summaries of accuracies of various quantities at: http://openmopac.net/manual/index_accuracy.html With the exception of most of the monatomic neutral species, i.e., atoms, e.g., H, He, etc., the heats of formation calculated by the methods in MOPAC are of limited accuracy. I hope this helps. Jimmy ( -#- -#- ) .-----------------oOOo----(_)----oOOo--------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: MrMOPAC-#-OpenMOPAC.net | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | http://openmopac.net/ | | USA | SKYPE: Jimmy.Stewart2 GMT 1500 - 0200| | .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo.| | .-----------------------\ (----( )---------------------------------------. \_) ) / (_/ From owner-chemistry@ccl.net Tue Mar 8 11:18:00 2011 From: "Hai Anh LE haianh(-)gmail.com" To: CCL Subject: CCL:G: open source software for molecular graph Message-Id: <-44073-110308054237-9492-INs/GECGzbFpxaaA9S8xjw=-=server.ccl.net> X-Original-From: Hai Anh LE Content-Type: multipart/alternative; boundary=bcaec517a9d6ce7cd9049df644fe Date: Tue, 8 Mar 2011 18:42:28 +0800 MIME-Version: 1.0 Sent to CCL by: Hai Anh LE [haianh**gmail.com] --bcaec517a9d6ce7cd9049df644fe Content-Type: text/plain; charset=ISO-8859-1 Do you have GaussView? Create a simple .gjf file with the xyz coorrdinates of the molecule, and open it with GaussView. Save the file (option geom=connectivity) is automatically chosen. Remember to tick Write to cartesians when you save it. Re-open the file again, the connectivity matrix is printed at the end of the file now. How it can be read can be easily found on the net. http://www.gaussian.com/g_tech/g_ur/k_geom.htm (look for keyword "connectivity"). Otherwise, it's very easy to write a little program to create the connectivity matrix (or adjacency matrix). But you need a database of bond lengths for this. Cheers, HA On 6 March 2011 20:04, Jinsong Zhao jszhao!A!yeah.net < owner-chemistry]=[ccl.net> wrote: > > Sent to CCL by: Jinsong Zhao [jszhao^^^yeah.net] > Hi there, > > I hope to convert a molecular structure in XYZ format (or any other format) > to a graph or an adjacency matrix. I have to use a open source software to > do such conversion, however, I find nothing by google. > > Would please to give me a hand? Any suggestions or comments will be really > appreciated. > > Regards, > Jinsonghttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Hai-Anh Le Department of Chemistry National University of Singapore --bcaec517a9d6ce7cd9049df644fe Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Do you have GaussView?

Create a simple .gjf file with th= e xyz coorrdinates of the molecule, and open it with GaussView. Save the fi= le (option geom=3Dconnectivity) is automatically chosen. Remember to tick W= rite to cartesians when you save it. Re-open the file again, the connectivi= ty matrix is printed at the end of the file now.

How it can be read can be easily found on the net.=A0


(look f= or keyword "connectivity").

Otherwise, i= t's very easy to write a little program to create the connectivity matr= ix (or adjacency matrix). But you need a database of bond lengths for this.=

Cheers,
HA

= On 6 March 2011 20:04, Jinsong Zhao jszhao!A!ye= ah.net <owner-chemistry]=[ccl.net> wrote:

Sent to CCL by: Jinsong Zhao [jszhao^^^yeah.net]
Hi there,

I hope to convert a molecular structure in XYZ format (or any other format)= to a graph or an adjacency matrix. I have to use a open source software to= do such conversion, however, I find nothing by google.

Would please to give me a hand? Any suggestions or comments will be really = appreciated.

Regards,
Jinsong



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--
Hai-Anh Le
Department of Chemistry
National University of Singapore

--bcaec517a9d6ce7cd9049df644fe-- From owner-chemistry@ccl.net Tue Mar 8 11:53:00 2011 From: "Bilel Mansouri bilelmansouri80],[yahoo.fr" To: CCL Subject: CCL:G: Problem with Gaussian 4 Au atom cluster calculations Message-Id: <-44074-110308095550-2683-kBcj5DeJaf8KcqDlvBZjuQ*o*server.ccl.net> X-Original-From: Bilel Mansouri Content-Type: multipart/alternative; boundary="0-831502471-1299596139=:84761" Date: Tue, 8 Mar 2011 14:55:39 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Bilel Mansouri [bilelmansouri80#yahoo.fr] --0-831502471-1299596139=:84761 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable *** Administrator (Jan Labanowski) changed the original "Subject: help"= *** to the one that in his opinion is more appropriate= > I'm doing a (what I thought was simple) test job of=A0four gold atoms(AU)= =A0molecules=A0using B3LYP > and the 6-31G basis set my input file is=20 =A0 %chk=3DAU4.chk # opt b3lyp/6-31g geom=3Dconnectivity =A0 Title Card Required =A0 0 1 =A0Au =A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 B1 =A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 B2=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = A1 =A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 B3=A0=A0=A0 2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = A2=A0=A0=A0 3=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1 =A0=A0 B1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.68562693 =A0=A0 B2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.63550597 =A0=A0 B3=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.78182728 =A0=A0 A1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 60.97439413 =A0=A0 A2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 118.27669862 =A0=A0 D1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.00000000 =A0 =A0 I have the error message =A0 --------------------------------------------------------------------- =A0Rotational constants (GHZ):=A0=A0=A0=A0=A0 0.2715100=A0=A0=A0=A0=A0 0.27= 15100=A0=A0=A0=A0=A0 0.1357550 =A0Standard basis: 3-21G (6D, 7F) =A03-21G basis sets are only available up to Xe. =A0Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 12:13:53 2= 011. =A0Job cpu time:=A0 0 days=A0 0 hours=A0 0 minutes=A0 1.0 seconds. =A0File lengths (MBytes):=A0 RWF=3D=A0=A0=A0=A0 12 Int=3D=A0=A0=A0=A0=A0 0 = D2E=3D=A0=A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 1 Scr=3D=A0=A0=A0=A0=A0 1 =A0=A0Any insight would be very helpful. =A0Thanks! =0A=0A=0A --0-831502471-1299596139=:84761 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable


> I'm doing a (what I thought= was simple) test job of four gold atoms(AU) molecules using= B3LYP
> and the 6-31G basis set
my input file is
 
%chk=3DAU4.chk
# opt b3lyp/6-31g geom=3Dconnectivity
 
T= itle Card Required
 
0 1
 Au
 Au  &nbs= p;            &= nbsp; 1           &n= bsp;  B1
 Au        &n= bsp;        2    &nb= sp;         B2    1&= nbsp;           &nbs= p; A1
 Au         &nbs= p;       1      = ;        B3    2 &nb= sp;            A2&nb= sp;   3            &= nbsp; D1

   B1        &nb= sp;    2.68562693
   B2    =          2.63550597
  = B3            = 2.78182728
   A1       &nb= sp;    60.97439413
   A2    = ;       118.27669862
   D1 =             0.000000= 00
 
 
I have the error message
 
---------------------------------------------------------------------<= BR> Rotational constants (GHZ):      0.271510= 0      0.2715100      0.1= 357550
 Standard basis: 3-21G (6D, 7F)
 3-21G basis sets ar= e only available up to Xe.
 Error termination via Lnk1e in C:\G03W\= l301.exe at Tue Mar 08 12:13:53 2011.
 Job cpu time:  0 days&n= bsp; 0 hours  0 minutes  1.0 seconds.
 File lengths (MByt= es):  RWF=3D     12 Int=3D    =   0 D2E=3D      0 Chk=3D   &nb= sp;  1 Scr=3D      1

  Any insight would be very helpful.

 Thanks!

=
=0A=0A=0A=0A=0A --0-831502471-1299596139=:84761-- From owner-chemistry@ccl.net Tue Mar 8 12:28:00 2011 From: "Zijun Yu zjyu*o*lamar.colostate.edu" To: CCL Subject: CCL:G: TS optimization problem Message-Id: <-44075-110308114539-6941-x68YGWakwLzuIgXNNzde1A(!)server.ccl.net> X-Original-From: "Zijun Yu" Date: Tue, 8 Mar 2011 11:45:36 -0500 Sent to CCL by: "Zijun Yu" [zjyu]-[lamar.colostate.edu] Dear All, I try to optimize the transition state using opt=TS. The input file is as below. %chk=ONIOMcasTSopt1.chk %mem=4000MB %nprocshared=4 #p oniom(casscf(8,5)/sto-3g:uff) opt=(ts,calcall,Noeigen,maxcycle=500) guess=read geom=check scf=(maxcycle=500) nosymm pop=full gfinput cas opt TS,read from TS1cas1 0 1 0 1 0 1 But calculation always died in L702. Does eneryone know what is wrong? Thank you! output file: Total kinetic energy from orbitals= 3.111412374459D+02 No NMR shielding tensors so no spin-rotation constants. Leave Link 601 at Tue Mar 8 10:39:00 2011, MaxMem= 524288000 cpu: 1.0 (Enter /usr/apps/chemistry/gaussian/g09_b01/Src/g09/l701.exe) Compute integral second derivatives. ... and contract with generalized density number 0. Leave Link 701 at Tue Mar 8 10:39:00 2011, MaxMem= 524288000 cpu: 0.0 (Enter /usr/apps/chemistry/gaussian/g09_b01/Src/g09/l702.exe) Compress NYI in L702. Error termination via Lnk1e in /usr/apps/chemistry/gaussian/g09_b01/Src/g09/l702.exe at Tue Mar 8 10:39:00 2011. Job cpu time: 0 days 0 hours 0 minutes 21.0 seconds. File lengths (MBytes): RWF= 102 Int= 0 D2E= 0 Chk= 3 Scr= 2 Job ran on Machine= From owner-chemistry@ccl.net Tue Mar 8 15:29:00 2011 From: "Alex M Clark aclark(_)molmatinf.com" To: CCL Subject: CCL: Reaction101 app released (iOS) Message-Id: <-44076-110308123634-26474-iNIp5ioffPjwO3lCiVzB6Q[A]server.ccl.net> X-Original-From: "Alex M Clark" Date: Tue, 8 Mar 2011 12:36:29 -0500 Sent to CCL by: "Alex M Clark" [aclark^^molmatinf.com] Molecular Materials Informatics and Eidogen-Sertanty have recently released a new app for iPhone/iPod/iPad, called Reaction101. The app is the result of a collaborative effort to come up with a new product with a specific focus, oriented toward the educational market. Reaction101 opens with an editor for chemical reactions, which consist of reactant, reagent and product components, which are in turn defined by structure diagram, name and stoichiometry. Structures can be drawn using the embedded Mobile Molecular DataSheet sketcher, or located by searching the Mobile Reagents database. Reactions can be balanced by manually specifying stoichiometry and observing the "residual atoms" display, or by using the automatic balancer. While only one reaction can be edited at any time, reactions can be stored using Eidogen-Sertanty's cloud-based servers, for subsequent recall. Also, a collection of common named reactions is available to all users, which can be used for reference, or as templates for drawing new reactions. High quality images for reactions can be copied onto the clipboard and used in other iOS apps (e.g. Keynote), or transmitted via email. Reaction data is also integrated into email attachments and internet downloads, allowing two-way data exchange. For more information, see: http://molmatinf.com/reaction101.html http://eidogen-sertanty.com/rxn101.html http://itunes.apple.com/us/app/reaction101/id423115765 From owner-chemistry@ccl.net Tue Mar 8 16:04:00 2011 From: "Manuel Melle Franco manuelmelle*|*gmail.com" To: CCL Subject: CCL:G: Problem with Gaussian 4 Au atom cluster calculations Message-Id: <-44077-110308125510-15979-LTWGvo9v0EpuGEdDzMOg9g**server.ccl.net> X-Original-From: Manuel Melle Franco Content-Type: multipart/alternative; boundary=0016e6475b94b2cc4b049dfc4f83 Date: Tue, 8 Mar 2011 17:54:41 +0000 MIME-Version: 1.0 Sent to CCL by: Manuel Melle Franco [manuelmelle###gmail.com] --0016e6475b94b2cc4b049dfc4f83 Content-Type: text/plain; charset=ISO-8859-1 actually the software gaussian has told you why, read carefully. regards Manuel ____________________________________________________________ Mohandas K. Gandhi often changed his mind publicly. An aide once asked him how he could so freely contradict this week what he had said just last week. The great man replied that it was because this week he knew better. ____________________________________________________________ Manuel Melle-Franco, Ph.D. Investigador Auxiliar do Requimte Theoretical and Computational Chemistry Group Chemistry Department Faculty of Sciences University of Porto Rua do Campo Alegre,687 4169-007 Porto Portugal. --------------------------------------------------------- A mind all logic is like a knife all blade. It makes the hand bleed that uses it. Rabindranath Tagore --------------------------------------------------------- On Tue, Mar 8, 2011 at 2:55 PM, Bilel Mansouri bilelmansouri80],[yahoo.fr < owner-chemistry(a)ccl.net> wrote: > > > > I'm doing a (what I thought was simple) test job of four gold > atoms(AU) molecules using B3LYP > > and the 6-31G basis set > my input file is > > %chk=AU4.chk > # opt b3lyp/6-31g geom=connectivity > > Title Card Required > > 0 1 > Au > Au 1 B1 > Au 2 B2 1 A1 > Au 1 B3 2 A2 > 3 D1 > > B1 2.68562693 > B2 2.63550597 > B3 2.78182728 > A1 60.97439413 > A2 118.27669862 > D1 0.00000000 > > > I have the error message > > --------------------------------------------------------------------- > Rotational constants (GHZ): 0.2715100 0.2715100 0.1357550 > Standard basis: 3-21G (6D, 7F) > 3-21G basis sets are only available up to Xe. > Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 12:13:53 > 2011. > Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. > File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 1 > Scr= 1 > > > Any insight would be very helpful. > > Thanks! > > > --0016e6475b94b2cc4b049dfc4f83 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable actually the software gaussian has told you why, read carefully.=A0
regards

Manuel
______= ______________________________________________________

Mohandas K. G= andhi often changed his mind publicly.=A0 An aide once asked
him how he could so freely contradict this week what he had said just
la= st week.=A0 The great man replied that it was because this week he knew
= better.

____________________________________________________________=

Manuel Melle-Franco, Ph.D.
Investigador Auxiliar do Requimte
Th= eoretical and Computational Chemistry Group
Chemistry Department
Facu= lty of Sciences
University of Porto
Rua do Campo Alegre,687
4169-0= 07 Porto
Portugal.
---------------------------------------------------------
<= br>A mind all logic is like a knife all blade. It makes the hand bleed that= uses it.
Rabindranath Tagore

-----------------------------------= ----------------------


On Tue, Mar 8, 2011 at 2:55 PM, Bilel Ma= nsouri bilelmansouri80],[yahoo.fr <owner-chemistry(a)ccl= .net> wrote:


--0016e6475b94b2cc4b049dfc4f83-- From owner-chemistry@ccl.net Tue Mar 8 16:39:00 2011 From: "Victor Rosas Garcia rosas.victor#%#gmail.com" To: CCL Subject: CCL:G: Problem with Gaussian 4 Au atom cluster calculations Message-Id: <-44078-110308131421-31556-Lxe+Zo4vUtScjk8dhjAMZg-,-server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=0015174be89033da0f049dfc9468 Date: Tue, 8 Mar 2011 12:14:10 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor.(~).gmail.com] --0015174be89033da0f049dfc9468 Content-Type: text/plain; charset=ISO-8859-1 Just what the error message says: "3-21G basis sets are only available up to Xe." So it cannot calculate Au because the basis set is not available, that is, Gaussian does not have this basis set for Au internally stored. Have a nice day! Victor 2011/3/8 Bilel Mansouri bilelmansouri80],[yahoo.fr > > > > I'm doing a (what I thought was simple) test job of four gold > atoms(AU) molecules using B3LYP > > and the 6-31G basis set > my input file is > > %chk=AU4.chk > # opt b3lyp/6-31g geom=connectivity > > Title Card Required > > 0 1 > Au > Au 1 B1 > Au 2 B2 1 A1 > Au 1 B3 2 A2 > 3 D1 > > B1 2.68562693 > B2 2.63550597 > B3 2.78182728 > A1 60.97439413 > A2 118.27669862 > D1 0.00000000 > > > I have the error message > > --------------------------------------------------------------------- > Rotational constants (GHZ): 0.2715100 0.2715100 0.1357550 > Standard basis: 3-21G (6D, 7F) > 3-21G basis sets are only available up to Xe. > Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 12:13:53 > 2011. > Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. > File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 1 > Scr= 1 > > > Any insight would be very helpful. > > Thanks! > > > --0015174be89033da0f049dfc9468 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Just what the error message says:

"3-21G basis sets are only av= ailable up to Xe."

So it cannot calculate Au because the basis = set is not available, that is, Gaussian does not have this basis set for Au= internally stored.

Have a nice day!

Victor

2011/3= /8 Bilel Mansouri bilelmansouri80],[yahoo.fr <owner-ch= emistry(~)ccl.net>

=
> I'm doing a (what I thought was simple) test job of=A0four gol= d atoms(AU)=A0molecules=A0using B3LYP
> and the 6-31G basis set
my input file is
=A0
%chk=3DAU4.chk
# opt b3lyp/6-31g geom=3Dconnectivity
=A0
Titl= e Card Required
=A0
0 1
=A0Au
=A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 B1
=A0Au= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 B2=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 A1
= =A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 B3=A0=A0=A0 2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = A2=A0=A0=A0 3=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1

=A0=A0 B1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.68562693
=A0=A0= B2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.63550597
=A0=A0 B3=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 2.78182728
=A0=A0 A1=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 60.97439413
=A0=A0 A2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 118.27669862<= br>=A0=A0 D1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.00000000
=A0
=A0
I have the error message
=A0
---------------------------------------------------------------------<= br>=A0Rotational constants (GHZ):=A0=A0=A0=A0=A0 0.2715100=A0=A0=A0=A0=A0 0= .2715100=A0=A0=A0=A0=A0 0.1357550
=A0Standard basis: 3-21G (6D, 7F)
= =A03-21G basis sets are only available up to Xe.
=A0Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 12:13:53 2= 011.
=A0Job cpu time:=A0 0 days=A0 0 hours=A0 0 minutes=A0 1.0 seconds.<= br>=A0File lengths (MBytes):=A0 RWF=3D=A0=A0=A0=A0 12 Int=3D=A0=A0=A0=A0=A0= 0 D2E=3D=A0=A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 1 Scr=3D=A0=A0=A0=A0=A0 1<= br>

=A0=A0Any insight would be very helpful.

=A0Thanks!



--0015174be89033da0f049dfc9468-- From owner-chemistry@ccl.net Tue Mar 8 17:14:00 2011 From: "WU Yanbin wuyb02 ~ gmail.com" To: CCL Subject: CCL:G: Monitoring basis set linear dependence in Gaussian Message-Id: <-44079-110308133113-9458-CvfYaKjXDQt5ufTCxTAHLA!^!server.ccl.net> X-Original-From: WU Yanbin Content-Type: multipart/alternative; boundary=e0cb4e43cf65509477049dfcd02f Date: Tue, 8 Mar 2011 12:30:59 -0600 MIME-Version: 1.0 Sent to CCL by: WU Yanbin [wuyb02=-=gmail.com] --e0cb4e43cf65509477049dfcd02f Content-Type: text/plain; charset=ISO-8859-1 Dear All, As far as my understanding, to eliminate basis set linear dependence problem, Gaussian would automatically remove the basis functions with eigenvalue less than some threshold in overlap matrix. Is there a keyword in Gaussian to check how many (or better what) basis sets are eliminated? Thank you. Best, Yanbin --e0cb4e43cf65509477049dfcd02f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,

As far as my understanding, to eliminate basis set linear = dependence problem, Gaussian would automatically remove the basis functions= with eigenvalue less than some threshold in overlap matrix. Is there a key= word in Gaussian to check how many (or better what) basis sets are eliminat= ed?

Thank you.

Best,
Yanbin
--e0cb4e43cf65509477049dfcd02f-- From owner-chemistry@ccl.net Tue Mar 8 17:49:00 2011 From: "Mehdi Esrafili m_esrafili!=!yahoo.com" To: CCL Subject: CCL:G: Problem with Gaussian 4 Au atom cluster calculations Message-Id: <-44080-110308133139-9721-MCMfOy9MFnnxximHOf+l7w#%#server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="0-898612051-1299609079=:81133" Date: Tue, 8 Mar 2011 10:31:19 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili{=}yahoo.com] --0-898612051-1299609079=:81133 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi=0AThe 3-21G basis set=A0does not work for Au atom. Use=A0a suitable=A0ba= sis set from =0Ahttps://bse.pnl.gov/bse/portal.=0A=A0=0ASincerely=0AMehdi= =A0=0A=A0=0A---------------------------------------------------------------= ---------------------------------------------------------------=A0=A0=0A=0A= `The man who makes no mistakes does not usually make anything.'=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=A0=A0=A0=A0 Edward John Phelps (1822-1900)=0A--------------------------= ---------------------------------------------------------------------------= -------------------------=0A =0AMehdi D. Esrafili=0AAssistant Professor of = Physical Chemistry=A0=0ACurrent address:=A0Department of Chemistry, =0AFacu= lty of Basic Sciences,University of=0AMargheh, Iran. =0AE-mail 1:m_esrafili= ],[yahoo.com=0AE-mail 2: esrafili],[maragheh.ac.ir=0A--------------------------= ---------------------------------------------------------------------------= -------------------------=0A =0A=0A=0A=0A=0A_______________________________= _=0AFrom: "Bilel Mansouri bilelmansouri80],[yahoo.fr" =0ATo: "Esrafili, Mehdi D " =0ASent: Tue,= March 8, 2011 6:25:39 PM=0ASubject: CCL:G: Problem with Gaussian 4 Au atom= cluster calculations=0A=0A=0A=0A=0A> I'm doing a (what I thought was simpl= e) test job of=A0four gold =0A>atoms(AU)=A0molecules=A0using B3LYP=0A> and = the 6-31G basis set=0Amy input file is =0A=A0=0A%chk=3DAU4.chk=0A# opt b3ly= p/6-31g geom=3Dconnectivity=0A=A0=0ATitle Card Required=0A=A0=0A0 1=0A=A0Au= =0A=A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 B1=0A=A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 B2=A0=A0=A0 1=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 A1=0A=A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 B3=A0=A0=A0 2=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 A2=A0=A0=A0 3=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 D1=0A=0A=A0=A0 B1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.685= 62693=0A=A0=A0 B2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.63550597=0A=A0=A0 B= 3=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.78182728=0A=A0=A0 A1=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0 60.97439413=0A=A0=A0 A2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 11= 8.27669862=0A=A0=A0 D1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.00000000=0A=A0= =0A=A0=0AI have the error message=0A=A0=0A---------------------------------= ------------------------------------=0A=A0Rotational constants (GHZ):=A0=A0= =A0=A0=A0 0.2715100=A0=A0=A0=A0=A0 0.2715100=A0=A0=A0=A0=A0 0.1357550=0A=A0= Standard basis: 3-21G (6D, 7F)=0A=A03-21G basis sets are only available up = to Xe.=0A=A0Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 1= 2:13:53 2011.=0A=A0Job cpu time:=A0 0 days=A0 0 hours=A0 0 minutes=A0 1.0 s= econds.=0A=A0File lengths (MBytes):=A0 RWF=3D=A0=A0=A0=A0 12 Int=3D=A0=A0= =A0=A0=A0 0 D2E=3D=A0=A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 1 =0AScr=3D=A0=A0= =A0=A0=A0 1=0A=0A=0A>=A0=A0Any insight would be very helpful.=0A>=0A>=0A>= =A0Thanks!=0A>=0A> =0A=0A=0A=0A --0-898612051-1299609079=:81133 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A
The 3-21G basis set does not work for Au atom. Use a suitabl= e basis set from https://bse.pnl.gov/bse= /portal.
=0A
 
=0A
Sincerely
=0A
Mehdi 
=0A
 
=0A
--------------------------= ---------------------------------------------------------------------------= -------------------------  
=0A
`The man who makes no mistakes does n= ot usually make anything.'
=0A
        =             &nb= sp;            = Edward John Phelps (1822-1900)
=0A
-------------------------------------------= ---------------------------------------------------------------------------= --------
Mehdi D. Esrafili
=0A
Assistant Professor of Physical Chemistry&nb= sp;
Current address: Department of Chemistry,
=0A
Fac= ulty of Basic Sciences,University of
=0A
Margheh, Iran.
=0A
E-mail 1: m_esrafili],[yahoo.com
E-mail 2:
esrafili],[maragheh.ac.ir<= /DIV>=0A
-------= ---------------------------------------------------------------------------= --------------------------------------------
=0A

=0A

=0A
= =0A
=0AFrom: "B= ilel Mansouri bilelmansouri80],[yahoo.fr" <owner-chemistry],[ccl.net>To: "Esrafili, Mehdi D -i= d#3za-" <m_esrafili],[yahoo.com>
Subject: CCL:G: Problem with Gaussian 4 Au atom cl= uster calculations

=0A


> I'm doing a (what I thought was simple) test job of= =A0four gold atoms(AU)=A0molecules=A0using B3LYP
> and the 6-31G basi= s set
my input file is
=A0
%chk=3DAU4.chk
# opt b3lyp/6-31g geom=3Dconnectivity
=A0
Titl= e Card Required
=A0
0 1
=A0Au
=A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 B1
=A0Au= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 B2=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 A1
= =A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 B3=A0=A0=A0 2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = A2=A0=A0=A0 3=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1

=A0=A0 B1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.68562693
=A0=A0= B2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.63550597
=A0=A0 B3=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 2.78182728
=A0=A0 A1=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 60.97439413
=A0=A0 A2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 118.27669862<= br>=A0=A0 D1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.00000000
=A0
=A0
I have the error message
=A0
---------------------------------------------------------------------<= br>=A0Rotational constants (GHZ):=A0=A0=A0=A0=A0 0.2715100=A0=A0=A0=A0=A0 0= .2715100=A0=A0=A0=A0=A0 0.1357550
=A0Standard basis: 3-21G (6D, 7F)
= =A03-21G basis sets are only available up to Xe.
=A0Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 12:13:53 2= 011.
=A0Job cpu time:=A0 0 days=A0 0 hours=A0 0 minutes=A0 1.0 seconds.<= br>=A0File lengths (MBytes):=A0 RWF=3D=A0=A0=A0=A0 12 Int=3D=A0=A0=A0=A0=A0= 0 D2E=3D=A0=A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 1 Scr=3D=A0=A0=A0=A0=A0 1<= br>

=A0=A0Any insight would be very helpful.

=A0Thanks!

=0A=0A=0A
=0A


> I'm doing a (what I thoug= ht was simple) test job of four gold atoms(AU) molecules usi= ng B3LYP
> and the 6-31G basis set
=0A
my input file is
=0A<= DIV> =0A
%chk=3DAU= 4.chk
# opt b3lyp/6-31g geom=3Dconnectivity
 
Title Card Requ= ired
 
0 1
 Au
 Au     =             1 &= nbsp;            B1<= BR> Au          &nbs= p;      2       = ;       B2    1  &nb= sp;           A1
 = ;Au            =      1        &= nbsp;     B3    2    = ;          A2   = ; 3            &= nbsp; D1
=0A

   B1        = ;     2.68562693
   B2   &n= bsp;         2.63550597
 &n= bsp; B3           &n= bsp; 2.78182728
   A1       = ;     60.97439413
   A2   &= nbsp;       118.27669862
   D1&n= bsp;            0.00= 000000
=0A
 
=0A
 
I have the error message
=0A
 
=0A-------------------= --------------------------------------------------
 Rotational cons= tants (GHZ):      0.2715100    = ;  0.2715100      0.1357550
 Standard= basis: 3-21G (6D, 7F)
 3-21G basis sets are only available up to X= e.
 Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 1= 2:13:53 2011.
 Job cpu time:  0 days  0 hours  0 min= utes  1.0 seconds.
 File lengths (MBytes):  RWF=3D &= nbsp;   12 Int=3D      0 D2E=3D &nb= sp;    0 Chk=3D      1 Scr=3D =      1
=0A
=0A=0A
=0A

  Any insight would be very helpful.
<= BR>
=0A
 Thanks!



=0A=0A --0-898612051-1299609079=:81133-- From owner-chemistry@ccl.net Tue Mar 8 18:24:00 2011 From: "William F. Coleman wcoleman+/-wellesley.edu" To: CCL Subject: CCL: Problem with Gaussian 4 Au atom cluster calculations Message-Id: <-44081-110308125719-18303-DMaBY7VuaJZ0VAMhiq/Tog_+_server.ccl.net> X-Original-From: "William F. Coleman" Content-Type: multipart/alternative; boundary="--=_--22f5dec3.22f5dd88.c99c1e74" Date: Tue, 08 Mar 2011 12:57:08 -0500 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman[-]wellesley.edu] This is a multi-part message in MIME format. ----=_--22f5dec3.22f5dd88.c99c1e74 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit "CCL Subscribers" writes: >> I'm doing a (what I thought was simple) test job of four gold >atoms(AU) molecules using B3LYP >> and the 6-31G basis set Au is not included in the 6-31G basis set (which goes through Kr). Try using LanL2MB instead. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html http://www.flicksstuff.com/photos/pictures.html new galleries 12/23/2010 ----=_--22f5dec3.22f5dd88.c99c1e74 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>
"CCL Subscribers" <chemistry=40ccl.net> writes:
> I'm doing a (what I thought was simple) test job of=C2= =A0four gold atoms(AU)=C2=A0molecules=C2=A0using B3LYP
> and the 6-31G basis set

Au is not included in the 6-31G basis= set (which goes through Kr).  Try using LanL2MB instead.

Cheers,

Flick

_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481



----=_--22f5dec3.22f5dd88.c99c1e74-- From owner-chemistry@ccl.net Tue Mar 8 19:00:00 2011 From: "Arindam Ganguly arindamganguly,gmail.com" To: CCL Subject: CCL:G: Problem with Gaussian 4 Au atom cluster calculations Message-Id: <-44082-110308130310-24189-Rd52WoffTPE8MTSdR+Pl+A|a|server.ccl.net> X-Original-From: Arindam Ganguly Content-Type: multipart/alternative; boundary=0016e6d58b41522aae049dfc6cbe Date: Tue, 8 Mar 2011 13:03:01 -0500 MIME-Version: 1.0 Sent to CCL by: Arindam Ganguly [arindamganguly[#]gmail.com] --0016e6d58b41522aae049dfc6cbe Content-Type: text/plain; charset=ISO-8859-1 Hi Bilel, The error message is self explanatory. It says clearly "3-21G basis sets are only available up to Xe." is not applicable for Au. Please refer to the EMSL Basis Set Exchange website where it is very well documented, what type of basis set is/are available for each atom in the periodic table. Thank you. Sincerely, Arindam On Tue, Mar 8, 2011 at 9:55 AM, Bilel Mansouri bilelmansouri80],[yahoo.fr < owner-chemistry-,-ccl.net> wrote: > > > > I'm doing a (what I thought was simple) test job of four gold > atoms(AU) molecules using B3LYP > > and the 6-31G basis set > my input file is > > %chk=AU4.chk > # opt b3lyp/6-31g geom=connectivity > > Title Card Required > > 0 1 > Au > Au 1 B1 > Au 2 B2 1 A1 > Au 1 B3 2 A2 > 3 D1 > > B1 2.68562693 > B2 2.63550597 > B3 2.78182728 > A1 60.97439413 > A2 118.27669862 > D1 0.00000000 > > > I have the error message > > --------------------------------------------------------------------- > Rotational constants (GHZ): 0.2715100 0.2715100 0.1357550 > Standard basis: 3-21G (6D, 7F) > 3-21G basis sets are only available up to Xe. > Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 12:13:53 > 2011. > Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. > File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 1 > Scr= 1 > > > Any insight would be very helpful. > > Thanks! > > > -- Arindam Ganguly, Ph.D. Postdoctoral Researcher University of Michigan, Ann Arbor Phone:-816-419-1806 http://www.linkedin.com/in/arindamganguly --0016e6d58b41522aae049dfc6cbe Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Bilel,
The error message is self explanatory. It says clearly "= 3-21G basis set= s are only available up to Xe." is not applicable for Au. Please refer= to the EMSL Basis Set Exchange website where it is very well=A0documented,= what type of basis set is/are available for each atom in the periodic tabl= e. Thank you.

Sin= cerely,
Arindam

On Tue, Mar 8, = 2011 at 9:55 AM, Bilel Mansouri bilelmansouri80],[yahoo.fr <owner-chemistry-,-ccl.net> wrote:




--
Arindam Ganguly, = Ph.D.
Postdoctoral Researcher
University of Michigan, Ann Arbor
Ph= one:-816-419-1806
http://www.linkedin.com/in/arindamganguly
--0016e6d58b41522aae049dfc6cbe-- From owner-chemistry@ccl.net Tue Mar 8 19:55:00 2011 From: "Zijun Yu zjyu__lamar.colostate.edu" To: CCL Subject: CCL:G: CASSCF problem Message-Id: <-44083-110308195339-18362-xBBwPnn+gjcOCqifGi3PHQ#server.ccl.net> X-Original-From: "Zijun Yu" Date: Tue, 8 Mar 2011 19:53:37 -0500 Sent to CCL by: "Zijun Yu" [zjyu*|*lamar.colostate.edu] Dear all, I try to do CASSCF calculation. The input file is as below. But it died with error. I don't know what the error message means? Does anyone know what is the problem? I appreciate for any help and suggestion. Thank you! input: %chk=aEXCITEa.chk %mem=4000MB %nprocshared=4 #p casscf(8,8,nroot=2)/sto-3g guess=read geom=check nosymm gfinput pop=full SCF=(maxcycle=500) excite state,read from cas2 0 1 output: Generating Lanczos Guess Non-zero components of Lanczos starting vector in hsort: 1 294 112 272 Defining IBUGAM 2ND ORD PT ENERGY CV -0.000518 CU -0.007375 UV -0.000011 TOTAL -1292.150187 WARNING! : large rotation I J = 84 83 Step scaled by 0.133595838661633 ITN= 1 MaxIt=500 E= -1292.1422837198 DE=-1.29D+03 Acc= 1.00D-08 Lan= 16 WARNING! : large rotation I J = 81 79 Step scaled by 0.519887013166195 ITN= 2 MaxIt=500 E= -1292.1439066687 DE=-1.62D-03 Acc= 1.00D-08 Lan= 20 Enter MCErr, Key1= 10 Key2= 1. ERROR MESSAGE FROM MCSCFERR .......... ERROR FOUND IN LANSEC .......... THERE ARE MORE EIVALS IN RANGE THAN FOUND BY EIVAL ROUTINE ......... PROGRAM STOPS Error 10 in MCVect. Error termination via Lnk1e in /usr/apps/chemistry/gaussian/g09_b01/Src/g09/l510.exe at Tue Mar 8 17:38:22 2011. Job cpu time: 0 days 0 hours 0 minutes 39.0 seconds. File lengths (MBytes): RWF= 137 Int= 0 D2E= 0 Chk= 2 Scr= 2 Job ran on Machine= From owner-chemistry@ccl.net Tue Mar 8 20:29:00 2011 From: "Acioli, Paulo p-acioli- -neiu.edu" To: CCL Subject: CCL:G: Problem with Gaussian 4 Au atom cluster calculations Message-Id: <-44084-110308170546-4608-m0zlEuFpBkvDHi426m//yA!=!server.ccl.net> X-Original-From: "Acioli, Paulo" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01CBDDDC.F49C80A9" Date: Tue, 8 Mar 2011 16:05:37 -0600 MIME-Version: 1.0 Sent to CCL by: "Acioli, Paulo" [p-acioli**neiu.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01CBDDDC.F49C80A9 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable You should read the manual and search for a basis set that is available for Au. In addition you might consider the use of a pseudopotential that generally includes some relativistic effects. =20 Paulo Acioli Northeastern Illinois University =20 ________________________________ > From: owner-chemistry+p-acioli=3D=3Dneiu.edu:+:ccl.net [mailto:owner-chemistry+p-acioli=3D=3Dneiu.edu:+:ccl.net] On Behalf Of = Victor Rosas Garcia rosas.victor#%#gmail.com Sent: Tuesday, March 08, 2011 12:14 PM To: Acioli, Paulo Subject: CCL:G: Problem with Gaussian 4 Au atom cluster calculations =20 Just what the error message says: "3-21G basis sets are only available up to Xe." So it cannot calculate Au because the basis set is not available, that is, Gaussian does not have this basis set for Au internally stored. Have a nice day! Victor 2011/3/8 Bilel Mansouri bilelmansouri80],[yahoo.fr > I'm doing a (what I thought was simple) test job of four gold atoms(AU) molecules using B3LYP > and the 6-31G basis set my input file is=20 =20 %chk=3DAU4.chk # opt b3lyp/6-31g geom=3Dconnectivity =20 Title Card Required =20 0 1 Au Au 1 B1 Au 2 B2 1 A1 Au 1 B3 2 A2 3 D1 B1 2.68562693 B2 2.63550597 B3 2.78182728 A1 60.97439413 A2 118.27669862 D1 0.00000000 =20 =20 I have the error message =20 --------------------------------------------------------------------- Rotational constants (GHZ): 0.2715100 0.2715100 0.1357550 Standard basis: 3-21G (6D, 7F) 3-21G basis sets are only available up to Xe. Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 12:13:53 2011. Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. File lengths (MBytes): RWF=3D 12 Int=3D 0 D2E=3D 0 = Chk=3D 1 Scr=3D 1 =09 Any insight would be very helpful. Thanks! =20 =20 =20 ------_=_NextPart_001_01CBDDDC.F49C80A9 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

You should read the manual and = search for a basis set that is available for Au. In addition you might consider the = use of a pseudopotential that generally includes some relativistic = effects.

 

Paulo = Acioli

Northeastern Illinois University

 


From: owner-chemistry+p-acioli=3D=3Dneiu.edu:+:ccl.net = [mailto:owner-chemistry+p-acioli=3D=3Dneiu.edu:+:ccl.net] On Behalf Of Victor Rosas = Garcia rosas.victor#%#gmail.com
Sent: Tuesday, March 08, = 2011 12:14 PM
To: Acioli, Paulo
Subject: CCL:G: Problem = with Gaussian 4 Au atom cluster calculations

 

Just what the = error message says:

"3-21G basis sets are only available up to Xe."

So it cannot calculate Au because the basis set is not available, that = is, Gaussian does not have this basis set for Au internally stored.

Have a nice day!

Victor

2011/3/8 Bilel Mansouri bilelmansouri80],[yahoo.fr <owner-chemistry*_*ccl.net&g= t;


=
> I'm doing a (what I thought was simple) test job of=A0four gol= d atoms(AU)=A0molecules=A0using B3LYP
> and the 6-31G basis set
my input file is
=A0
%chk=3DAU4.chk
# opt b3lyp/6-31g geom=3Dconnectivity
=A0
Titl= e Card Required
=A0
0 1
=A0Au
=A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 B1
=A0Au= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 B2=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 A1
= =A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 B3=A0=A0=A0 2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = A2=A0=A0=A0 3=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1

=A0=A0 B1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.68562693
=A0=A0= B2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.63550597
=A0=A0 B3=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 2.78182728
=A0=A0 A1=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 60.97439413
=A0=A0 A2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 118.27669862<= br>=A0=A0 D1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.00000000
=A0
=A0
I have the error message
=A0
---------------------------------------------------------------------<= br>=A0Rotational constants (GHZ):=A0=A0=A0=A0=A0 0.2715100=A0=A0=A0=A0=A0 0= .2715100=A0=A0=A0=A0=A0 0.1357550
=A0Standard basis: 3-21G (6D, 7F)
= =A03-21G basis sets are only available up to Xe.
=A0Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 12:13:53 2= 011.
=A0Job cpu time:=A0 0 days=A0 0 hours=A0 0 minutes=A0 1.0 seconds.<= br>=A0File lengths (MBytes):=A0 RWF=3D=A0=A0=A0=A0 12 Int=3D=A0=A0=A0=A0=A0= 0 D2E=3D=A0=A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 1 Scr=3D=A0=A0=A0=A0=A0 1<= br>

=A0=A0Any insight would be very helpful.

=A0Thanks!



> I'm doing a (what I thought was simple) test job of four = gold atoms(AU) molecules using B3LYP
> and the 6-31G basis set

my input file is =

 

%chk=3DAU4.chk
# opt b3lyp/6-31g geom=3Dconnectivity
 
Title Card Required
 
0 1
 Au
=  Au           = ;      = 1            =   B1
=  Au           = ;      = 2            =   B2    = 1            =   A1
=  Au           = ;      = 1            =   B3    = 2            =   A2    = 3            =   D1


   = B1            = ; 2.68562693
   = B2            = ; 2.63550597
   = B3            = ; 2.78182728
   A1            60.97439413
   = A2           118.27669862
   = D1            = ; 0.00000000

 

 
I have the error message

 

----------------------------------------------= -----------------------
 Rotational constants (GHZ):      0.2715100      0.2715100      0.1357550
 Standard basis: 3-21G (6D, 7F)
 3-21G basis sets are only available up to Xe.
 Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 = 12:13:53 2011.
 Job cpu time:  0 days  0 hours  0 minutes  = 1.0 seconds.
 File lengths (MBytes):  RWF=3D     12 Int=3D      0 = D2E=3D      0 Chk=3D      1 = Scr=3D      1


  Any insight would be very = helpful.

 Thanks!

 

 

 

------_=_NextPart_001_01CBDDDC.F49C80A9-- From owner-chemistry@ccl.net Tue Mar 8 21:04:00 2011 From: "Arindam Ganguly arindamganguly!^!gmail.com" To: CCL Subject: CCL:G: Problem with Gaussian 4 Au atom cluster calculations Message-Id: <-44085-110308181157-6025-T08lkNJdpyCC7L2T68jD7A%%server.ccl.net> X-Original-From: Arindam Ganguly Content-Type: multipart/alternative; boundary=001485f46e8cabf095049e00bc96 Date: Tue, 8 Mar 2011 18:11:49 -0500 MIME-Version: 1.0 Sent to CCL by: Arindam Ganguly [arindamganguly[-]gmail.com] --001485f46e8cabf095049e00bc96 Content-Type: text/plain; charset=ISO-8859-1 Hi Bilel, The error message is self explanatory. It says clearly "3-21G basis sets are only available up to Xe." is not applicable for Au. Please refer to the EMSL Basis Set Exchange website where it is very well documented, what type of basis set is/are available for each atom in the periodic table. Thank you. Sincerely, Arindam On Tue, Mar 8, 2011 at 9:55 AM, Bilel Mansouri bilelmansouri80],[yahoo.fr < owner-chemistry(!)ccl.net> wrote: > > > > I'm doing a (what I thought was simple) test job of four gold > atoms(AU) molecules using B3LYP > > and the 6-31G basis set > my input file is > > %chk=AU4.chk > # opt b3lyp/6-31g geom=connectivity > > Title Card Required > > 0 1 > Au > Au 1 B1 > Au 2 B2 1 A1 > Au 1 B3 2 A2 > 3 D1 > > B1 2.68562693 > B2 2.63550597 > B3 2.78182728 > A1 60.97439413 > A2 118.27669862 > D1 0.00000000 > > > I have the error message > > --------------------------------------------------------------------- > Rotational constants (GHZ): 0.2715100 0.2715100 0.1357550 > Standard basis: 3-21G (6D, 7F) > 3-21G basis sets are only available up to Xe. > Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 12:13:53 > 2011. > Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. > File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 1 > Scr= 1 > > > Any insight would be very helpful. > > Thanks! > > > -- Arindam Ganguly, Ph.D. Postdoctoral Researcher University of Michigan, Ann Arbor Phone:-816-419-1806 http://www.linkedin.com/in/arindamganguly --001485f46e8cabf095049e00bc96 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Bilel,
The error messag= e is self explanatory. It says clearly "3-21G basis sets are only available up to Xe." is not applicable fo= r Au. Please refer to the EMSL Basis Set Exchange website where it is very = well=A0documented, what type of basis set is/are available for each atom in= the periodic table. Thank you.

Sincerely,
Arindam

On Tue, Mar 8, 2011 at 9:55 AM, Bilel Mansouri bilelmansou= ri80],[yahoo.fr <owner-chemistry(!)ccl.net> wrote:




--
Arindam Ganguly, = Ph.D.
Postdoctoral Researcher
University of Michigan, Ann Arbor
Ph= one:-816-419-1806
http://www.linkedin.com/in/arindamganguly
--001485f46e8cabf095049e00bc96--

=
> I'm doing a (what I thought was simple) test job of=A0four gol= d atoms(AU)=A0molecules=A0using B3LYP
> and the 6-31G basis set
my input file is
=A0
%chk=3DAU4.chk
# opt b3lyp/6-31g geom=3Dconnectivity
=A0
Titl= e Card Required
=A0
0 1
=A0Au
=A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 B1
=A0Au= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 B2=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 A1
= =A0Au=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 B3=A0=A0=A0 2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = A2=A0=A0=A0 3=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1

=A0=A0 B1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.68562693
=A0=A0= B2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.63550597
=A0=A0 B3=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 2.78182728
=A0=A0 A1=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 60.97439413
=A0=A0 A2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 118.27669862<= br>=A0=A0 D1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.00000000
=A0
=A0
I have the error message
=A0
---------------------------------------------------------------------<= br>=A0Rotational constants (GHZ):=A0=A0=A0=A0=A0 0.2715100=A0=A0=A0=A0=A0 0= .2715100=A0=A0=A0=A0=A0 0.1357550
=A0Standard basis: 3-21G (6D, 7F)
= =A03-21G basis sets are only available up to Xe.
=A0Error termination via Lnk1e in C:\G03W\l301.exe at Tue Mar 08 12:13:53 2= 011.
=A0Job cpu time:=A0 0 days=A0 0 hours=A0 0 minutes=A0 1.0 seconds.<= br>=A0File lengths (MBytes):=A0 RWF=3D=A0=A0=A0=A0 12 Int=3D=A0=A0=A0=A0=A0= 0 D2E=3D=A0=A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 1 Scr=3D=A0=A0=A0=A0=A0 1<= br>

=A0=A0Any insight would be very helpful.

=A0Thanks!