From owner-chemistry@ccl.net Fri Mar 5 08:43:00 2010 From: "Ron Bakus rbakus*chem.ucsb.edu" To: CCL Subject: CCL:G: Error in G03 E.01 nmr(giao,mixed) calculation Message-Id: <-41373-100305004454-31997-Ymz8G3Q15w1PQGkqpXPbtA/a\server.ccl.net> X-Original-From: "Ron Bakus" Date: Fri, 5 Mar 2010 00:44:50 -0500 Sent to CCL by: "Ron Bakus" [rbakus*chem.ucsb.edu] I can confirm that the ECP's are making it into the first part (I see the pseudopotentials in the log file). The LANL08 set is, in fact, not built in, but I retrieved them from EMSL, and Im fairly sure that the syntax is fine (I dont see any warnings about atoms missing basis sets). -Ron > "Jamin Krinsky jamink a berkeley.edu" wrote: > > Sent to CCL by: Jamin Krinsky [jamink ~~ berkeley.edu] > --0016364270fe802ce80480ffdc4d > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Ron, > It looks like Gaussian cannot read your ECPs from the checkpoint file, e.g. > it's dying in link301. Is it possible that the ECPs didn't make it into the > first part either (due to a syntax error, you didn't supply the exact input > syntax you used)? That calculation would run but give you nonsense results. > Look in the "Pseudopotential Parameters" section of the output for the first > step and verify that there are indeed ECPs read in. I don't recognize that > ECP as a built-in GO3 option. > Jamin > > > On Thu, Mar 4, 2010 at 10:35 AM, Ronald Bakus rbakus%chem.ucsb.edu < > owner-chemistry!=!ccl.net> wrote: > > > > > Sent to CCL by: "Ronald Bakus" [rbakus###chem.ucsb.edu] > > When running a nmr(giao,mixed) calculation, the first step completes fine > > [the Fermi contacts], but when it proceeds to the second step, the job > > terminates with the following error: Unrecognized value of NGIC in SetDat. > > Please note that im not interested at all in the values of the S and Br > > shifts, and for the sake of efficiency was using ECP's for them. > > > > Sample input: > > %chk=checkpoint.chk > > %mem=120MW > > %nprocshared=4 > > #p nmr(giao,mixed) b3lyp/genecp geom=connectivity formcheck > > > > mol specifications > > > > C H 0 > > 6-311+g(2df,2pd) > > **** > > N 0 > > 6-311+g(d,p) > > **** > > LANL 08 S basis set > > **** > > LANL 08 Br basis set > > **** > > > > LANL08 S and Br ECPS > > > > Output: > > * > > Fermi Contact (FC) contribution to K (Hz) > > * > > Normal termination of Gaussian 03 at Thu Mar 4 04:35:26 2010. > > (Enter g03/l1.exe) > > Link1: Proceeding to internal job step number 2. > > ---------------------------------------------------------------------- > > #P Geom=AllCheck Guess=Read SCRF=Check GenChk RB3LYP/ChkBas NMR=ReadFC > > IOp(3/6=22) > > ---------------------------------------------------------------------- > > * > > Rotational constants (GHZ): 0.5463627 0.1168917 0.0983431 > > Leave Link 202 at Thu Mar 4 04:35:31 2010, MaxMem= 125829120 cpu: > > 0.1 > > Basis read from chk: checkpoint.chk (5D, 7F) > > Pseudo-potential data read from chk file. > > Unrecognized value of NGIC in SetDat. > > Error termination via Lnk1e in g03/l301.exe > > > > Has anyone seen something like this before? Is Gaussian having a fit due > > my use of ECPs? > > > > Any insight would be appreciated > > Thanks, > > Ron Bakus> > > > > > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink!=!berkeley.edu, 510-643-0616 > http://glab.cchem.berkeley.edu > > --0016364270fe802ce80480ffdc4d > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > > Dear Ron,
It looks like Gaussian cannot read your ECPs from the checkpoi= > nt file, e.g. it's dying in link301. Is it possible that the ECPs didn&= > #39;t make it into the first part either (due to a syntax error, you didn&#= > 39;t supply the exact input syntax you used)? That calculation would run bu= > t give you nonsense results. Look in the "Pseudopotential Parameters&q= > uot; section of the output for the first step and verify that there are ind= > eed ECPs read in. I don't recognize that ECP as a built-in GO3 option.<= > br> > Jamin


On Thu, Mar 4, 2010 at 10:35 AM= > , Ronald Bakus rbakus%chem.ucsb.edu pan dir=3D"ltr"><owner-chemis= > try!=!ccl.net> wrote:
>
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
> Sent to CCL by: "Ronald =A0Bakus" [rbakus### m.ucsb.edu" target=3D"_blank">chem.ucsb.edu]
> When running a nmr(giao,mixed) calculation, the first step completes fine [= > the Fermi contacts], but when it proceeds to the second step, the job termi= > nates with the following error: Unrecognized value of NGIC in SetDat. =A0Pl= > ease note that im not interested at all in the values of the S and Br shift= > s, and for the sake of efficiency was using ECP's for them.
> >
> Sample input:
> %chk=3Dcheckpoint.chk
> %mem=3D120MW
> %nprocshared=3D4
> #p nmr(giao,mixed) b3lyp/genecp geom=3Dconnectivity formcheck
>
> mol specifications
>
> C H 0
> 6-311+g(2df,2pd)
> ****
> N 0
> 6-311+g(d,p)
> ****
> LANL 08 S basis set
> ****
> LANL 08 Br basis set
> ****
>
> LANL08 S and Br ECPS
>
> Output:
> *
> Fermi Contact (FC) contribution to K (Hz)
> *
> Normal termination of Gaussian 03 at Thu Mar =A04 04:35:26 2010.
> =A0(Enter g03/l1.exe)
> =A0Link1: =A0Proceeding to internal job step number =A02.
> =A0---------------------------------------------------------------------- r> > =A0#P Geom=3DAllCheck Guess=3DRead SCRF=3DCheck GenChk RB3LYP/ChkBas NMR=3D= > ReadFC
> =A0IOp(3/6=3D22)
> =A0---------------------------------------------------------------------- r> > *
> Rotational constants (GHZ): =A0 =A0 =A00.5463627 =A0 =A0 =A00.1168917 =A0 = > =A0 =A00.0983431
> =A0Leave Link =A0202 at Thu Mar =A04 04:35:31 2010, MaxMem=3D =A0125829120 = > cpu: =A0 =A0 =A0 0.1
> =A0Basis read from chk: checkpoint.chk (5D, 7F)
> =A0Pseudo-potential data read from chk file.
> =A0Unrecognized value of NGIC in SetDat.
> =A0Error termination via Lnk1e in g03/l301.exe
>
> Has anyone seen something like this before? =A0Is Gaussian having a fit due= > my use of ECPs?
>
> Any insight would be appreciated
> Thanks,
> Ron Bakus
>
>
>
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--
Jamin L Krinsky, Ph.D.<= > br>Molecular Graphics and Computation Facility
175 Tan Hall, University = > of California, Berkeley, CA 94720
>jamink!=!berkeley.edu, 510-643-0616
> http://glab.cchem.berkeley.edu a>

> > --0016364270fe802ce80480ffdc4d-- > > From owner-chemistry@ccl.net Fri Mar 5 09:18:00 2010 From: "Krishna B S bskimo*|*gmail.com" To: CCL Subject: CCL: Cp-M-Cp bond angle Message-Id: <-41374-100305082502-32438-/Uwc7qogDMMO1pFcXLoQEw,server.ccl.net> X-Original-From: "Krishna B S" Date: Fri, 5 Mar 2010 08:24:58 -0500 Sent to CCL by: "Krishna B S" [bskimo_._gmail.com] Dear CCL Members, Can anyone tell me, how to view the Cp(centroid)-M-Cp(centroide) Bond Angle from the optimized geometry?... Thanks in advance... krishna From owner-chemistry@ccl.net Fri Mar 5 09:54:00 2010 From: "Radoslaw Kaminski rkaminski.rk(!)gmail.com" To: CCL Subject: CCL: Cp-M-Cp bond angle Message-Id: <-41375-100305095305-18971-f7pAhTN6qYC52uv+MfeQCg(-)server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=000e0ce0d602a83f1404810ede28 Date: Fri, 5 Mar 2010 09:52:51 -0500 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk||gmail.com] --000e0ce0d602a83f1404810ede28 Content-Type: text/plain; charset=ISO-8859-1 Hi, What does it mean to view? You can calculate the centroids and than the angle. I don't understand the problem to be honest... Cheers, Radek 2010/3/5 Krishna B S bskimo*|*gmail.com > > Sent to CCL by: "Krishna B S" [bskimo_._gmail.com] > Dear CCL Members, > > Can anyone tell me, how to view the Cp(centroid)-M-Cp(centroide) Bond > Angle from the optimized geometry?... > > Thanks in advance... > > krishna> > > --000e0ce0d602a83f1404810ede28 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

What does it mean to view? You can calculate the centroids and t= han the angle. I don't understand the problem to be honest...

Ch= eers,

Radek

2010/3/5 Krishna B S b= skimo*|*gmail.com <owner-chemistry(_)ccl.net>

Sent to CCL by: "Krishna B S" [bskimo_._gmail.com]
Dear CCL Members,

=A0Can anyone tell me, how to view the Cp(centroid)-M-Cp(centroide) Bond A= ngle from the optimized geometry?...

Thanks in advance...

krishna



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--000e0ce0d602a83f1404810ede28-- From owner-chemistry@ccl.net Fri Mar 5 11:26:01 2010 From: "Abrash, Sam sabrash.,.richmond.edu" To: CCL Subject: CCL: Hydrogen Bond Message-Id: <-41376-100305111705-878-Lde0Ek0IJ9YKJN6fhRcipw,server.ccl.net> X-Original-From: "Abrash, Sam" Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 5 Mar 2010 09:52:28 -0500 MIME-Version: 1.0 Sent to CCL by: "Abrash, Sam" [sabrash[*]richmond.edu] PM2 and other force field methods are not reliable for hydrogen bonds. Whi= le there is controversy about the use of DFT methods to treat hydrogen bond= s, Truhlar did an extensive review several years ago indicating that some o= f the functionals are able to treat them quite well. I strongly recommend = finding and referring to that review. Methods like the Moller-Plesset pert= urbation theory and CCSD are extremely reliable, although both are more com= putationally expensive (both CPU and hard disk). Your basis sets are proba= bly fine, although you should probably test them by doing at least a test c= alculation with a larger basis set and making sure that there are no signif= icant changes. Be careful with the use of the correlation consistent basis sets for hydrog= en bonds. They are unusually compact, so the effect of augmentation is not= as large as in the case of the Pople basis sets. Sometimes additional aug= mentation is required. Finally it is worthwhile to explore doing the counterpoise corrections for = your geometries and energies to account for basis set superposition error. I hope this is of some assistance. Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash .. richmond.edu Web-page: http://oncampus.richmond.edu/~sabrash =20 "In 1893 Charles Hinton left Japan to become a mathematics instructor at Pr= inceton University, where he invented a baseball-pitching machine that used= gunpowder to propel the balls, like a cannon. After several accidents, th= e device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian St= eward and Jack Cohen, The Science of Diskworld III=20 -----Original Message----- > From: owner-chemistry+sabrash=3D=3Drichmond.edu .. ccl.net [mailto:owner-chemi= stry+sabrash=3D=3Drichmond.edu .. ccl.net] On Behalf Of S Bill s_bill36#,#yaho= o.co.uk Sent: Thursday, March 04, 2010 11:31 PM To: Abrash, Sam Subject: CCL: Hydrogen Bond Sent to CCL by: "S Bill" [s_bill36##yahoo.co.uk] Dear CCL I have two molecules forming hydrogen bond, I want to calculate energy of t= hat=20 bond. I calculated it using B3LYP and PM2 methods, and 6-311+G** and aug-cc= - pVDZ diffuse as basis set. In case, B3LYP and PM2 with 6-311+G** I got different values. In case, PM2 = with =20 aug-cc-pVDZ, the SCF convergence not completed even if I increase SCF cycle= s to=20 more than 1000 cycle. Why it doesn't converge? And which method and basis s= et=20 do you recommend. Thanks in advance S. Bill -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Mar 5 13:11:01 2010 From: "Lochana C Menikarachchi lochanac[#]yahoo.com" To: CCL Subject: CCL: GEPOL_Surface Message-Id: <-41377-100305130940-18940-8u7wwAD5DAkaqMmeXtamnw:server.ccl.net> X-Original-From: "Lochana C Menikarachchi" Date: Fri, 5 Mar 2010 13:09:37 -0500 Sent to CCL by: "Lochana C Menikarachchi" [lochanac[]yahoo.com] Hello Everyone, Does anybody know a software that can display a surface generated with gepol. Or any conversion utility where I can convert gepol surface to some other format which can be visualized with another program. Thanks. From owner-chemistry@ccl.net Fri Mar 5 21:46:01 2010 From: "keetch keetch keeetch^^yahoo.com" To: CCL Subject: CCL: Cp-M-Cp bond angle Message-Id: <-41378-100305125124-17793-CFZb8NSgysV8KSsEUi7gNw(0)server.ccl.net> X-Original-From: keetch keetch Content-Type: multipart/alternative; boundary="0-1681959648-1267807872=:53583" Date: Fri, 5 Mar 2010 16:51:12 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: keetch keetch [keeetch(-)yahoo.com] --0-1681959648-1267807872=:53583 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL members, =A0 =A0=A0=A0 I have calculated the centroids and got the angle. I have sent th= e post to know whether it is possible to get the Cg-M-Cg angle directly fro= m=A0any programmes, which can calculate the centroids automatically. I am s= orry for the inconvenience. =A0 Krishna --- On Fri, 5/3/10, Radoslaw Kaminski rkaminski.rk(!)gmail.com wrote: > From: Radoslaw Kaminski rkaminski.rk(!)gmail.com Subject: CCL: Cp-M-Cp bond angle To: "Bellie, Krishnamoorthy Sundaram " Date: Friday, 5 March, 2010, 8:22 PM Hi, What does it mean to view? You can calculate the centroids and than the ang= le. I don't understand the problem to be honest... Cheers, Radek 2010/3/5 Krishna B S bskimo*|*gmail.com Sent to CCL by: "Krishna B S" [bskimo_._gmail.com] Dear CCL Members, =A0Can anyone tell me, how to view the Cp(centroid)-M-Cp(centroide) Bond An= gle from the optimized geometry?... Thanks in advance... krishna -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY++ccl.net or use: =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST++ccl.net or use =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml=A0 =A0 =A0http://www.ccl.net/spammers.txt=0A=0A=0A The INTERNET now has a personality. YOURS! See your Yahoo! H= omepage. http://in.yahoo.com/ --0-1681959648-1267807872=:53583 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCL members,
 
    I have calculated the centroids and got the angle. = I have sent the post to know whether it is possible to get the Cg-M-Cg angl= e directly from any programmes, which can calculate the centroids auto= matically. I am sorry for the inconvenience.
 
Krishna


--- On Fri, 5/3/10, Radoslaw Kaminski rkaminski.rk(!)gmail.= com <owner-chemistry+/-ccl.net> wrote:

From: Radoslaw Kaminski rkaminski.rk(!)gmail.com = <owner-chemistry+/-ccl.net>
Subject: CCL: Cp-M-Cp bond angle
To: = "Bellie, Krishnamoorthy Sundaram " <keeetch+/-yahoo.com>
Dat= e: Friday, 5 March, 2010, 8:22 PM

Hi,

What does it mean to view? You can calcu= late the centroids and than the angle. I don't understand the problem to be= honest...

Cheers,

Radek

2010/3/5 Krishna B S bskimo*|*gmail.com <= owner-chemistry++ccl.net>

Sent to CCL by: "K= rishna B S" [bskimo_._gmail.com]
Dear CCL Members,

 Can anyone tell = me, how to view the Cp(centroid)-M-Cp(centroide) Bond Angle from the optimi= zed geometry?...

Thanks in advance...

krishna



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E-mail to subscribers: CHEMISTRY++ccl.net or use:
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= =0A=0A=0A=0A
=0AThe INTERNET now has a pers= onality. YOURS! See your Yahoo! Homepage. --0-1681959648-1267807872=:53583-- From owner-chemistry@ccl.net Fri Mar 5 22:39:01 2010 From: "Radoslaw Kaminski rkaminski.rk,,gmail.com" To: CCL Subject: CCL: Cp-M-Cp bond angle Message-Id: <-41379-100305223758-9151-ZBCuJCzELHhkoX6fnf7Ycg++server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=00c09f8017d9873d3f0481197a8f Date: Fri, 5 Mar 2010 22:32:16 -0500 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk++gmail.com] --00c09f8017d9873d3f0481197a8f Content-Type: text/plain; charset=ISO-8859-1 Hi, I'm a crystallographer but programs like Diamond, PLATON or maybe Mercury can do it very easily. I use Diamond 3 and it can read different types of files like e.g. XYZ ones so it can be used also with theoretical data. Mercury also. I'm sure there are lots of such programs. Is this answer your question at least partially? I don't know programs which could recognize Cp rings automatically and calculate appropriate angles, unfortunately. Cheers, Radek 2010/3/5 keetch keetch keeetch^^yahoo.com > Dear CCL members, > > I have calculated the centroids and got the angle. I have sent the post > to know whether it is possible to get the Cg-M-Cg angle directly from any > programmes, which can calculate the centroids automatically. I am sorry for > the inconvenience. > > Krishna > > > --- On *Fri, 5/3/10, Radoslaw Kaminski rkaminski.rk(!)gmail.com > * wrote: > > > From: Radoslaw Kaminski rkaminski.rk(!)gmail.com > > Subject: CCL: Cp-M-Cp bond angle > To: "Bellie, Krishnamoorthy Sundaram " > Date: Friday, 5 March, 2010, 8:22 PM > > Hi, > > What does it mean to view? You can calculate the centroids and than the > angle. I don't understand the problem to be honest... > > Cheers, > > Radek > > 2010/3/5 Krishna B S bskimo*|*gmail.com > > > >> >> Sent to CCL by: "Krishna B S" [bskimo_._gmail.com] >> Dear CCL Members, >> >> Can anyone tell me, how to view the Cp(centroid)-M-Cp(centroide) Bond >> Angle from the optimized geometry?... >> >> Thanks in advance... >> >> krishna>> >> E-mail to subscribers: CHEMISTRY++ccl.netor use:>> >> E-mail to administrators: CHEMISTRY-REQUEST++ccl.netor use>> >> >> > > ------------------------------ > The INTERNET now has a personality. YOURS! See your Yahoo! Homepage > . --00c09f8017d9873d3f0481197a8f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

I'm a crystallographer but programs like Diamond, PLATON or = maybe Mercury can do it very easily. I use Diamond 3 and it can read differ= ent types of files like e.g. XYZ ones so it can be used also with theoretic= al data. Mercury also. I'm sure there are lots of such programs. Is thi= s answer your question at least partially? I don't know programs which = could recognize Cp rings automatically and calculate appropriate angles, un= fortunately.

Cheers,

Radek


2010/3/5 kee= tch keetch keeetch^^yahoo.com <owner-chemistry..ccl.ne= t>
Dear CCL members,
=A0
=A0=A0=A0 I have calculated the centroids and got the angle. I have se= nt the post to know whether it is possible to get the Cg-M-Cg angle directl= y from=A0any programmes, which can calculate the centroids automatically. I= am sorry for the inconvenience.
=A0
Krishna


--- On Fri, 5/3/10, Radoslaw Kaminski rkaminski.rk(!)gmail.com <owner-chemist= ry||ccl.net> wr= ote:

From: Radoslaw Kaminski rkaminski.rk(!)gmail.com <owner-chemistry||= ccl.net>
Subject: CCL: Cp-M-Cp bond angle
To: "Bellie, Krishnamoorthy Sundar= am " <keeetch||yahoo= .com>
Date: Friday, 5 March, 2010, 8:22 PM

Hi,

What does it mean to view? You can calculate the centroids = and than the angle. I don't understand the problem to be honest...
<= br>Cheers,

Radek

2010/3/5 Krishna B S bskimo*|*gmail.com <owner-chemistry++ccl.ne= t>

Sent to CCL b= y: "Krishna B S" [bskimo_._gmail.com]
Dear CCL Members,

=A0Can anyone tell me, how to view the Cp(centroid= )-M-Cp(centroide) Bond Angle from the optimized geometry?...

Thanks = in advance...

krishna



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