From owner-chemistry@ccl.net Mon Jul 9 07:10:01 2007
From: "Carlos Silva Lopez csilval^uvigo.es" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL:G: Nuclear repulsion energy
Message-Id: <-34688-070709070403-17234-nGKUu6FoHtOlR+BXQHOw8g#server.ccl.net>
X-Original-From: Carlos Silva Lopez <csilval a uvigo.es>
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Date: Mon, 09 Jul 2007 13:02:08 +0200
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Sent to CCL by: Carlos Silva Lopez [csilval^uvigo.es]
Hi CCLers,
Perhaps this is a dumb question, but I have come to this observation I
cannot quite explain. The nuclear repulsion energy obtained for the same
geometry with 3 different codes is uncomfortably different. Is there any
explanation to this?:
G03: 2415.9379779077 Hartrees
GAMESS (US) 22Nov 2004: 2415.9381648177
ORCA 2.6: 2415.8913723108 Eh
My coordinates are:
C -1.434100 1.172214 -0.511956
C -2.181985 2.234035 -1.012304
C -1.608613 3.002788 -2.031486
C -0.336160 2.723942 -2.541720
C 0.402873 1.654375 -2.030463
C -0.156178 0.883949 -1.015498
H -3.170884 2.453751 -0.634807
H -2.177650 3.831553 -2.441786
H 0.073829 3.333722 -3.340039
H 1.389606 1.432155 -2.428665
C 0.413823 -0.288027 -0.270177
N -1.748668 0.223468 0.496948
C -0.827998 -0.855573 0.457720
C 1.438186 -1.252792 -0.935380
H -0.667452 -1.304760 1.432671
C -2.764062 0.203213 1.451205
O -2.851208 -0.659506 2.295058
O -3.597283 1.251026 1.317891
H -4.274510 1.152227 2.013056
C 2.455664 -0.964523 0.196581
H 1.767045 -0.902403 -1.914589
H 1.112584 -2.287982 -1.012839
C 3.858815 -0.488203 -0.132331
H 2.555493 -1.797377 0.906043
N 1.540767 0.069944 0.721565
C 1.663052 0.959016 1.683027
O 4.387641 -1.129715 -1.155770
O 4.447090 0.364143 0.523742
H 5.315743 -0.840314 -1.280866
O 0.583725 1.593349 2.067568
O 2.778375 1.241621 2.280917
H 0.817996 2.292019 2.710143
Br -1.611074 -2.443806 -0.649844
H 3.574491 0.922904 1.728071
Thanks!
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Carlos Silva Lopez IPP Researcher
Universidad de Vigo Phone : (+34) 986813721
Departmento de Qu�mica Org�nica Fax : (+34) 986812262
Campus Universitario e-mail: csilval##uvigo.es
36310 Vigo, Pontevedra
http://riesling.chem.umn.edu/~carlos
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From owner-chemistry@ccl.net Mon Jul 9 09:29:00 2007
From: "Crawford, Daniel crawdad() vt.edu" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL:G: Nuclear repulsion energy
Message-Id: <-34689-070709083900-20668-kSWujfcLvggAhShPOq37wQ^-^server.ccl.net>
X-Original-From: "Crawford, Daniel" <crawdad~~vt.edu>
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Date: Mon, 9 Jul 2007 08:05:43 -0400
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Sent to CCL by: "Crawford, Daniel" [crawdad|vt.edu]
Your coordinates appear to be in Angstroms, so this is very likely a result
of differences in the Bohr <-> Angstrom conversion factor among the three
codes.
-TDC
On 7/9/07 7:02 AM, "Carlos Silva Lopez csilval^uvigo.es"
<owner-chemistry(~)ccl.net> wrote:
>
> Sent to CCL by: Carlos Silva Lopez [csilval^uvigo.es]
> Hi CCLers,
>
> Perhaps this is a dumb question, but I have come to this observation I
> cannot quite explain. The nuclear repulsion energy obtained for the same
> geometry with 3 different codes is uncomfortably different. Is there any
> explanation to this?:
>
> G03: 2415.9379779077 Hartrees
> GAMESS (US) 22Nov 2004: 2415.9381648177
> ORCA 2.6: 2415.8913723108 Eh
>
> My coordinates are:
>
> C -1.434100 1.172214 -0.511956
> C -2.181985 2.234035 -1.012304
> C -1.608613 3.002788 -2.031486
> C -0.336160 2.723942 -2.541720
> C 0.402873 1.654375 -2.030463
> C -0.156178 0.883949 -1.015498
> H -3.170884 2.453751 -0.634807
> H -2.177650 3.831553 -2.441786
> H 0.073829 3.333722 -3.340039
> H 1.389606 1.432155 -2.428665
> C 0.413823 -0.288027 -0.270177
> N -1.748668 0.223468 0.496948
> C -0.827998 -0.855573 0.457720
> C 1.438186 -1.252792 -0.935380
> H -0.667452 -1.304760 1.432671
> C -2.764062 0.203213 1.451205
> O -2.851208 -0.659506 2.295058
> O -3.597283 1.251026 1.317891
> H -4.274510 1.152227 2.013056
> C 2.455664 -0.964523 0.196581
> H 1.767045 -0.902403 -1.914589
> H 1.112584 -2.287982 -1.012839
> C 3.858815 -0.488203 -0.132331
> H 2.555493 -1.797377 0.906043
> N 1.540767 0.069944 0.721565
> C 1.663052 0.959016 1.683027
> O 4.387641 -1.129715 -1.155770
> O 4.447090 0.364143 0.523742
> H 5.315743 -0.840314 -1.280866
> O 0.583725 1.593349 2.067568
> O 2.778375 1.241621 2.280917
> H 0.817996 2.292019 2.710143
> Br -1.611074 -2.443806 -0.649844
> H 3.574491 0.922904 1.728071
>
>
> Thanks!
--
T. Daniel Crawford Department of Chemistry
crawdad(~)vt.edu Virginia Tech
Voice: 540-231-7760 FAX: 540-231-3255 Blacksburg, Virginia 24061
--------------------
http://www.chem.vt.edu/chem-dept/crawford/
From owner-chemistry@ccl.net Mon Jul 9 10:04:00 2007
From: "errol lewars elewars]=[trentu.ca" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: TDDFT problems with squarine molecule
Message-Id: <-34690-070708101143-11337-3FGNnPUlwe5pwOlFssdnsQ^-^server.ccl.net>
X-Original-From: errol lewars <elewars-,-trentu.ca>
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Date: Sun, 08 Jul 2007 10:11:49 -0400
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Sent to CCL by: errol lewars [elewars . trentu.ca]
2007 July 8
Read this paper and see if it's of any help:
Y. Zhao, D. G. Truhlar, J Phys Chem A, 2006, 110(49), 13126
E. Lewars
====
Arvydas Tamulis tamulis##mserv.itpa.lt wrote:
>
> Sent to CCL by: Arvydas Tamulis [tamulis^-^mserv.itpa.lt]
> Dear Colleagues,
>
> We have TDDFT problems with intermolecular electron charge transfer
> (ICT) complex containing exotic squarine molecule and other van der Waals
> forces bonded electron acceptor molecule.
> Which DFT potential and basis set you will recommend for squarine
> molecule
> which possesses four 90 valence bond angles in the center (i.e. possesses
> high strains)?
>
> With best regards,
> Arvydas Tamulishttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences:
> http://server.ccl.net/chemistry/announcements/conferences/>
>
>
From owner-chemistry@ccl.net Mon Jul 9 10:38:01 2007
From: "Shobe, David David.Shobe++sud-chemie.com" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL:G: Frequency symmetry problem
Message-Id: <-34691-070709094731-1665-ntvk4sX+U8Gi8D2ZbVlWYw=server.ccl.net>
X-Original-From: "Shobe, David" <David.Shobe]*[sud-chemie.com>
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Sent to CCL by: "Shobe, David" [David.Shobe^sud-chemie.com]
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Mike,
=20
Any symmetry label with a ? means that the orbital/vibrational mode does
not neatly belong to any symmetry class. Usually this results from one
or more orbitals having a small percentage of another orbital (of a
different symmetry) mixed in, due to rounding errors. For example, an
orbital may be 99.95% pi and 0.05% sigma. Similarly a vibrational mode
may have a small amount of another vibrational mode (of different
symmetry) mixed in.=20=20
=20
I always end up having to animate vibrational modes of interest anyway,
and you can then see the true nature of the vibrational mode and which
symmetry class it should belong to.
=20
--David Shobe
=20
________________________________
> From: owner-chemistry[#]ccl.net [mailto:owner-chemistry[#]ccl.net]=20
Sent: Saturday, July 07, 2007 1:51 PM
To: Shobe, David
Subject: CCL:G: Frequency symmetry problem
=20
Dear CCL users
I have perform Opt+Freq calculation with Gaussian 03 and the frequency
symmetry obtained is ?A. what does this mean and how do I formally
represent this frequency symmetry.
Any help will be greatly appreciated
thanks
mike
=20=20
________________________________
Building a website is a piece of cake.=20
Yahoo! Small Business gives you all the tools to get online.
<http://us.rd.yahoo.com/evt=3D48251/*http:/smallbusiness.yahoo.com/webhost
ing/?p=3DPASSPORTPLUS>=20
This e-mail message may contain confidential and / or privileged informatio=
n. If you are not an addressee or otherwise authorized to receive this mess=
age, you should not use, copy, disclose or take any action based on this e-=
mail or any information contained in the message. If you have received this=
material in error, please advise the sender immediately by reply e-mail an=
d delete this message.=20
Thank you.
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<div class=3DSection1>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Mike,<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Any symmetry label with a ? means that=
the
orbital/vibrational mode does not neatly belong to any symmetry class. =
; Usually
this results from one or more orbitals having a small percentage of another
orbital (of a different symmetry) mixed in, due to rounding errors. F=
or
example, an orbital may be 99.95% pi and 0.05% sigma. Similarly a
vibrational mode may have a small amount of another vibrational mode (of
different symmetry) mixed in. <o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
=3D'font-size:
10.0pt;font-family:Arial;color:navy'>I always end up having to animate
vibrational modes of interest anyway, and you can then see the true nature =
of
the vibrational mode and which symmetry class it should belong to.<o:p></o:=
p></span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
=3D'font-size:
10.0pt;font-family:Arial;color:navy'>--David Shobe<o:p></o:p></span></font>=
</p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><font siz=
e=3D3
face=3D"Times New Roman"><span style=3D'font-size:12.0pt'>
<hr size=3D2 width=3D"100%" align=3Dcenter tabindex=3D-1>
</span></font></div>
<p class=3DMsoNormal><b><font size=3D2 face=3DTahoma><span style=3D'font-si=
ze:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=3D2
face=3DTahoma><span style=3D'font-size:10.0pt;font-family:Tahoma'> owner-ch=
emistry[#]ccl.net
[mailto:owner-chemistry[#]ccl.net] <br>
<b><span style=3D'font-weight:bold'>Sent:</span></b> Saturday, July 07, 200=
7 1:51
PM<br>
<b><span style=3D'font-weight:bold'>To:</span></b> Shobe, David<br>
<b><span style=3D'font-weight:bold'>Subject:</span></b> CCL:G: Frequency sy=
mmetry
problem</span></font><o:p></o:p></p>
</div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span style=3D=
'font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span style=3D=
'font-size:
12.0pt'>Dear CCL users<br>
<br>
I have perform Opt+Freq calculation with Gaussian 03 and the frequency symm=
etry
obtained is ?A. what does this mean and how do I formally represent this
frequency symmetry.<br>
Any help will be greatly appreciated<br>
thanks<br>
mike<o:p></o:p></span></font></p>
<p><font size=3D3 face=3D"Times New Roman"><span style=3D'font-size:12.0pt'=
> <o:p></o:p></span></font></p>
<div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><font siz=
e=3D3
face=3D"Times New Roman"><span style=3D'font-size:12.0pt'>
<hr size=3D1 width=3D"100%" align=3Dcenter>
</span></font></div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span style=3D=
'font-size:
12.0pt'>Building a website is a piece of cake. <br>
Yahoo! Small Business gives you <a
href=3D"http://us.rd.yahoo.com/evt=3D48251/*http:/smallbusiness.yahoo.com/w=
ebhosting/?p=3DPASSPORTPLUS">all
the tools to get online.</a><o:p></o:p></span></font></p>
</div>
<DIV>
This e-mail message may contain confidential and / or privileged informatio=
n. If you are not an addressee or otherwise authorized to receive this mess=
age, you should not use, copy, disclose or take any action based on this e-=
mail or any information contained in the message. If you have received this=
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d delete this message. <BR>
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From owner-chemistry@ccl.net Mon Jul 9 11:15:00 2007
From: "bala bala:+:igib.res.in" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL: review/article on hydration changes
Message-Id: <-34692-070709095339-6576-VFPmwo7j3vq4oXMs2HPLpw\a/server.ccl.net>
X-Original-From: "bala" <bala() igib.res.in>
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Date: Mon, 9 Jul 2007 19:16:19 +0530
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Sent to CCL by: "bala" [bala__igib.res.in]
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Can some please write me about any review/articles/book which covers in =
detail about the energetics involved in hydration changes during a =
duplex formation in solution from single nucleic acid strands.
Thanks in advance,
Bala
------_=_NextPart_001_01C7C22F.8793DB1F
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"><HTML =
DIR=3Dltr><HEAD><META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Diso-8859-1"></HEAD><BODY><DIV><FONT face=3D'Arial' =
color=3D#000000 size=3D2>=0A=
<P><FONT size=3D2>Can some please write me about any =
review/articles/book =0A=
which covers in detail about the energetics involved in hydration =
changes during =0A=
a duplex formation in solution from single nucleic acid =
strands.<BR><BR>Thanks =0A=
in advance,<BR>Bala<BR></FONT></P></FONT></DIV></BODY></HTML>
------_=_NextPart_001_01C7C22F.8793DB1F--
From owner-chemistry@ccl.net Mon Jul 9 11:49:00 2007
From: "Carlos Silva Lopez csilval-$-uvigo.es" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: ANSWER TO: Nuclear repulsion energy
Message-Id: <-34693-070709102025-27705-ui+blySKpQ3Q1biC0HaDcQ!^!server.ccl.net>
X-Original-From: Carlos Silva Lopez <csilval^^uvigo.es>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Mon, 09 Jul 2007 16:19:04 +0200
MIME-Version: 1.0
Sent to CCL by: Carlos Silva Lopez [csilval:-:uvigo.es]
Thanks to Daniel Crawford, Abdul-Rahman ALLOUCHE, Jeff Hammond and
perhaps others that already sent a response but I still did not received
their mails.
Eventually source of the energy discrepancies was the conversion factor
> from Angstroms to Bohrs. Doing the calculation in bohrs provided the
exact same repulsion energy for the three codes.
Best regards
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Carlos Silva Lopez IPP Researcher
Universidad de Vigo Phone : (+34) 986813721
Departmento de Qu�mica Org�nica Fax : (+34) 986812262
Campus Universitario e-mail: csilval#,#uvigo.es
36310 Vigo, Pontevedra
http://riesling.chem.umn.edu/~carlos
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From owner-chemistry@ccl.net Mon Jul 9 13:02:00 2007
From: "Frank Neese neese(0)thch.uni-bonn.de" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL:G: Nuclear repulsion energy
Message-Id: <-34694-070709124040-27904-JtA0oc4p6NXAzzogeimbEw##server.ccl.net>
X-Original-From: Frank Neese <neese*thch.uni-bonn.de>
Content-Type: text/plain; charset="us-ascii"; format=flowed
Date: Mon, 09 Jul 2007 18:40:24 +0200
Mime-Version: 1.0
Sent to CCL by: Frank Neese [neese]*[thch.uni-bonn.de]
>
>Sent to CCL by: "Crawford, Daniel" [crawdad|vt.edu]
>Your coordinates appear to be in Angstroms, so this is very likely a result
>of differences in the Bohr <-> Angstrom conversion factor among the three
>codes.
... we have checked it and this is exactly correct. The difference
seems large but it is an accumulation of small differences. The
present default orca value for au differs in the fifth digit from the
latest value in the handbook of chemical and physics which is
presumably what Gaussian uses (i don't know and i cannot check since
we are banned by Gaussian). We have taken the opportunity to update
our natural constants to their latest values. In any case, in order
to ensure that different quantum chemical codes give the same answers
one should input atomic units anyways.
Best regards,
FN
From owner-chemistry@ccl.net Mon Jul 9 19:54:00 2007
From: "Lochana C Menikarachchi lochanac[*]yahoo.com" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL:G: Oniom_Calculation
Message-Id: <-34695-070709162833-19272-CoDX24wEm6RT32d5Bs+cvw[#]server.ccl.net>
X-Original-From: "Lochana C Menikarachchi" <lochanac!=!yahoo.com>
Date: Mon, 9 Jul 2007 16:28:29 -0400
Sent to CCL by: "Lochana C Menikarachchi" [lochanac . yahoo.com]
Dear Keerthi,
You may have to define additional bond stretching and angle bending parameters. These parameters should come after the connectivity section of the gaussian input file. For example if you are using link atoms when partitioning the system, parameters for those connections should appear in the gaussian input file. Hope this will help. Good luck!
Lochana C. Menikarachchi
UConn
http://gascon.chem.uconn.edu
From owner-chemistry@ccl.net Mon Jul 9 20:29:00 2007
From: "Lochana C Menikarachchi lochanac[-]yahoo.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL:G: Oniom_Calc
Message-Id: <-34696-070709190120-12204-gb9EHjL0WCtMD5NZ66Sw1w^_^server.ccl.net>
X-Original-From: "Lochana C Menikarachchi" <lochanac a yahoo.com>
Date: Mon, 9 Jul 2007 19:01:16 -0400
Sent to CCL by: "Lochana C Menikarachchi" [lochanac*yahoo.com]
Dear Keerthi,
You may have to define additional bond stretching and angle bending parameters. These parameters should come after the connectivity section of the gaussian input file. For example if you are using link atoms when partitioning the system, parameters for those connections should appear in the gaussian input file. Hope this will help. Good luck!
Lochana C. Menikarachchi
UConn
From owner-chemistry@ccl.net Mon Jul 9 21:09:00 2007
From: "lochana menikarachchi lochanac_-_yahoo.com" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL:G: oniom calculation
Message-Id: <-34697-070709171711-26991-V3d4n1TmY2r55b/z+h+w1g-,-server.ccl.net>
X-Original-From: lochana menikarachchi <lochanac===yahoo.com>
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Sent to CCL by: lochana menikarachchi [lochanac]~[yahoo.com]
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Dear Keerthi,
You may have to define additional bond stretching and angle bending parameters. These parameters should come after the connectivity section of the gaussian input file. For example if you are using link atoms when partitioning the system, parameters for those connections should appear in the gaussian input file. Hope this will help. Good luck!
Lochana C. Menikarachchi
UConn
http://gascon.chem.uconn.edu
"Keerthi Jayasundera jaya0046(_)d.umn.edu" <owner-chemistry##ccl.net> wrote:
Sent to CCL by: "Keerthi Jayasundera" [jaya0046^d.umn.edu]
I am a beginner to oniom I am trying an oniom calculation for a peptide chain with a triazole ring in the middle. I always get an error message in the middle of the calculation.
As a start I used a 3-layer oniom as given in the gaussian tutorial. So I got a message saying that same parameter is missing to a N atom in the high layer.
Anyway I found that could come with the "Amber" So I changed it to UFF in the low layer. Now I get some other error which does not give any understandable message.
I think I have not used commands correctly. Please someone help me to solve the problem
Here is my input file.
%chk=quick.chk
%mem=6MW
%nproc=1
opt=rcfc oniom(rhf/6-31g:ram1:amber) geom=connectivity
Title Card Required
0 1 0 1 0 1 0 1 0 1 0 1
C-CM- 0 -0.979628 -1.159218 0.000009 H
C-CM- 0 0.422122 -1.159218 0.000009 H
H-H4- 0 1.066495 -2.031924 0.000034 M H-H4 2
N- 0 -0.310937 1.003031 -0.000095 H
N-N2- 0 0.846120 0.211578 0.000009 H
N-N3--0.516300 0 -1.419355 0.161290 0.000000 H
C-CT-0.039700 0 -2.859630 0.320067 0.000068 H
H-H1-0.110500 0 -3.277620 -0.150672 -0.889757 M H-H1 7
C-CT-0.056000 0 -3.483217 -0.326921 1.232208 M H-H1 7
C-C-0.536600 0 -3.248651 1.791511 0.000147 M H-H1 7
H-HC--0.017300 0 -3.250175 -1.391678 1.241385 M
H-HC--0.017300 0 -3.081256 0.140223 2.131266 M
C-CT-0.013600 0 -4.981165 -0.140179 1.195083 M
O-O--0.581900 0 -2.355867 2.678364 0.000146 M
H-HC--0.042500 0 -5.215008 0.924407 1.186354 M
H-HC--0.042500 0 -5.383929 -0.607494 0.296474 M
C-C-0.805400 0 -5.605570 -0.788016 2.428839 M
O-O2--0.818800 0 -5.734708 -0.067706 3.454547 M
O-O2--0.818800 0 -5.947450 -1.997018 2.333810 M
N-N--0.415700 0 -4.667286 2.176705 0.000223 M
H-H-0.271900 0 -5.358580 1.538797 0.339614 M
C-CT--0.087500 0 -5.063971 3.480727 -0.491479 M
H-H1-0.096900 0 -4.580882 4.256153 0.103028 M
C-CT-0.298500 0 -4.660558 3.663221 -1.950786 L H-H1 22
C-C-0.597300 0 -6.571867 3.665676 -0.399129 L H-H1 22
H-HC--0.029700 0 -3.578481 3.570399 -2.043492 L
C-CT--0.319200 0 -5.336934 2.594335 -2.802621 L
C-CT--0.319200 0 -5.094761 5.044582 -2.429256 L
O-O--0.567900 0 -7.292069 2.741987 0.060956 L
H-HC-0.079100 0 -6.419114 2.686824 -2.710783 L
H-HC-0.079100 0 -5.048915 2.724325 -3.845812 L
H-HC-0.079100 0 -5.026906 1.606779 -2.460984 L
H-HC-0.079100 0 -4.611580 5.808946 -1.820665 L
H-HC-0.079100 0 -4.806645 5.175545 -3.472299 L
H-HC-0.079100 0 -6.176850 5.137991 -2.337278 L
N-N--0.516300 0 -7.186941 4.923315 -0.847381 L
H-H-0.293600 0 -6.651063 5.581231 -1.376513 L
C-CT-0.039700 0 -8.569717 5.209666 -0.522518 L
H-H1-0.110500 0 -9.210774 4.437288 -0.947463 L
C-CT-0.056000 0 -8.783229 5.244046 0.987069 L
C-C-0.536600 0 -8.996294 6.558691 -1.083453 L
H-HC--0.017300 0 -8.518191 4.276855 1.414148 L
H-HC--0.017300 0 -8.154675 6.018939 1.425887 L
C-CT-0.013600 0 -10.233003 5.544569 1.283615 L
O-O--0.581900 0 -8.175766 7.258267 -1.732221 L
H-HC--0.042500 0 -10.498670 6.511888 0.857216 L
H-HC--0.042500 0 -10.862188 4.769803 0.845477 L
C-C-0.805400 0 -10.446796 5.578994 2.795182 L
O-O2--0.818800 0 -10.298521 6.688991 3.372697 L
O-O2--0.818800 0 -10.756343 4.494968 3.357912 L
N-N--0.415700 0 -10.366797 7.044417 -0.867366 L
H-H-0.271900 0 -10.957507 6.593282 -0.198382 L
C-CT--0.002400 0 -10.861782 8.176899 -1.623723 L
H-H1-0.097800 0 -10.239071 9.048695 -1.422967 L
C-CT--0.034300 0 -10.832645 7.891714 -3.121536 L
C-C-0.597300 0 -12.297546 8.506169 -1.240775 L
H-HC-0.029500 0 -9.808555 7.685743 -3.432851 L
H-HC-0.029500 0 -11.459040 7.026711 -3.339479 L
C-CA-0.011800 0 -11.331632 9.017578 -3.995345 L
O-O--0.567900 0 -12.888752 7.820305 -0.366912 L
C-CA--0.125600 0 -11.350562 8.867789 -5.387180 L
C-CA--0.125600 0 -11.775340 10.211216 -3.413663 L
H-HA-0.133000 0 -11.005104 7.938457 -5.840061 L
C-CA--0.170400 0 -11.813199 9.911636 -6.197334 L
C-CA--0.170400 0 -12.237977 11.255063 -4.223817 L
H-HA-0.133000 0 -11.760602 10.327838 -2.330020 L
H-HA-0.143000 0 -11.827938 9.795014 -7.280977 L
C-CA--0.107200 0 -12.256907 11.105274 -5.615652 L
H-HA-0.143000 0 -12.583435 12.184395 -3.770936 L
H-HA-0.129700 0 -12.617104 11.917984 -6.246414 L
N-N--0.347900 0 -12.993637 9.625381 -1.891714 L
H-H-0.274700 0 -12.550033 10.125419 -2.635473 L
C-CT--0.263700 0 -14.322568 10.004049 -1.455647 L
H-H1-0.156000 0 -15.001717 9.161287 -1.584520 L
C-CT--0.000700 0 -14.323143 10.410005 0.014326 L
C-C-0.734100 0 -14.849615 11.181352 -2.263524 L
H-HC-0.032700 0 -13.982173 9.572662 0.623175 L
H-HC-0.032700 0 -13.654477 11.258795 0.157651 L
C-CT-0.039000 0 -15.736543 10.800370 0.433298 L
O-O2--0.589400 0 -14.141789 11.688069 -3.172254 L
H-HC-0.028500 0 -16.078044 11.638013 -0.174841 L
H-HC-0.028500 0 -16.405741 9.951881 0.290683 L
C-CT-0.048600 0 -15.737119 11.206327 1.903273 L
H-H1-0.068700 0 -15.396149 10.368984 2.512121 L
H-H1-0.068700 0 -15.068452 12.055116 2.046597 L
N-N2--0.529500 0 -17.095392 11.592620 2.346300 L
H-H-0.345600 0 -17.850021 11.554247 1.676106 L
C-CA-0.807600 0 -17.367676 11.987984 3.586642 L
N-N2--0.862700 0 -16.427662 12.064208 4.524438 L
N-N2--0.862700 0 -18.624431 12.312365 3.876888 L
H-H-0.447800 0 -15.474243 11.817145 4.300713 L
H-H-0.447800 0 -16.671555 12.368807 5.456015 L
H-H-0.447800 0 -19.335864 12.253370 3.162407 L
H-H-0.447800 0 -18.861600 12.616204 4.810447 L
O-OH- 0 -16.149152 11.711677 -1.989919 L
H-HO- 0 -16.493627 12.138214 -2.777956 L
C-CT- 0 -1.971529 -2.337238 0.000148 H
H-H1- 0 -2.312409 -2.516359 0.998454 M H-H1 97
H-H1- 0 -2.807007 -2.100096 -0.624865 M H-H1 97
N-N- 0 -1.302226 -3.541423 -0.512564 H
H-H- 0 -1.939344 -4.059457 -1.083284 M H-H 100
C-C-0.597300 0 -0.864453 -4.376461 0.615251 M H-H 100
C-CT--0.024900 0 -0.037047 -5.628013 0.359323 M
O-O--0.567900 0 -1.173802 -4.056507 1.792326 M
N-N--0.415700 0 0.287099 -6.301875 1.600469 M
H-H1-0.084300 0 0.882942 -5.339427 -0.149046 M
C-CT-0.211700 0 -0.840250 -6.536712 -0.565206 M
H-H-0.271900 0 -0.030927 -5.926491 2.471070 M
H-H1-0.035200 0 -0.257411 -7.428659 -0.795052 M
H-H1-0.035200 0 -1.768812 -6.826793 -0.073551 M
O-OH--0.654600 0 -1.140564 -5.838678 -1.776594 M
H-HO-0.427500 0 -1.646188 -6.410710 -2.358593 L H-HO 111
C-C-0.597300 0 1.083440 -7.537316 1.579817 M
C-CT--0.059700 0 1.182562 -8.399803 2.829927 L H-H2 113
O-O--0.567900 0 1.683197 -7.881810 0.528539 L H-H1 113
N-N--0.415700 0 2.011332 -9.565021 2.595383 L
H-H1-0.086900 0 0.179485 -8.717971 3.114015 L
C-CT-0.130300 0 1.787312 -7.563573 3.952701 L
H-H-0.271900 0 2.427990 -9.709793 1.697922 L
H-HC-0.018700 0 1.840278 -8.160662 4.863074 L
C-CT--0.320400 0 3.190484 -7.117729 3.555261 L
C-CT--0.043000 0 0.915074 -6.337240 4.199546 L
H-HC-0.088200 0 3.138271 -6.520160 2.645160 L
H-HC-0.088200 0 3.623208 -6.519964 4.357462 L
H-HC-0.088200 0 3.814318 -7.993944 3.378686 L
H-HC-0.023600 0 0.862007 -5.739377 3.289687 L
H-HC-0.023600 0 -0.088004 -6.655407 4.483633 L
C-CT--0.066000 0 1.519823 -5.501009 5.322319 L
H-HC-0.018600 0 2.522801 -5.182068 5.038746 L
H-HC-0.018600 0 0.896743 -4.624314 5.499167 L
H-HC-0.018600 0 1.572790 -6.098098 6.232692 L
C-C-0.536600 0 2.239625 -10.534308 3.676709 L
C-CT-0.039700 0 3.284848 -11.628043 3.510163 L
O-O--0.581900 0 1.570859 -10.459764 4.740083 L
N-N--0.516300 0 3.349503 -12.471304 4.686740 L
H-H1-0.110500 0 4.255202 -11.160138 3.344097 L
C-CT-0.056000 0 2.917005 -12.439652 2.272582 L
H-H-0.293600 0 2.749247 -12.289694 5.465655 L
H-HC--0.017300 0 3.668607 -13.211525 2.107031 L
H-HC--0.017300 0 1.943386 -12.906989 2.420098 L
C-CT-0.013600 0 2.860022 -11.527101 1.070874 L
H-HC--0.042500 0 2.108260 -10.755186 1.235505 L
H-HC--0.042500 0 3.833481 -11.059722 0.922437 L
C-C-0.805400 0 2.491696 -12.339774 -0.168330 L
O-O2--0.818800 0 1.266381 -12.454522 -0.438582 L
O-O2--0.818800 0 3.439166 -12.838062 -0.832867 L
C-C-0.597300 0 4.297472 -13.593752 4.735361 L
C-CT--0.024900 0 4.292558 -14.543002 5.925061 L
O-O--0.567900 0 5.113049 -13.769784 3.793332 L
N-N3--0.415700 0 5.300035 -15.573477 5.774352 L
H-H1-0.084300 0 3.307903 -15.004749 5.998170 L
C-CT-0.211700 0 4.537363 -13.715592 7.182473 L
H-H-0.271900 0 5.883024 -15.587765 4.961997 L
H-H1-0.035200 0 4.505016 -14.364945 8.057342 L
H-H1-0.035200 0 5.515908 -13.239521 7.119974 L
O-OH--0.654600 0 3.525587 -12.711534 7.296830 L
H-HO-0.427500 0 3.679694 -12.190672 8.088381 L
H-H-0.271900 0 5.412337 -16.270352 6.482698 L
1 2 2.0 6 1.0 97 1.0
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Dear Keerthi,<br><br>You may have to define additional bond stretching and angle bending parameters. These parameters should come after the connectivity section of the gaussian input file. For example if you are using link atoms when partitioning the system, parameters for those connections should appear in the gaussian input file. Hope this will help. Good luck!<br><br>Lochana C. Menikarachchi<br>UConn<br>http://gascon.chem.uconn.edu<br><br><br><br><b><i>"Keerthi Jayasundera jaya0046(_)d.umn.edu" <owner-chemistry##ccl.net></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> <br>Sent to CCL by: "Keerthi Jayasundera" [jaya0046^d.umn.edu]<br>I am a beginner to oniom I am trying an oniom calculation for a peptide chain with a triazole ring in the middle. I always get an error message in the middle of the calculation.<br>As a start I used a 3-layer oniom as given in the gaussian
tutorial. So I got a message saying that same parameter is missing to a N atom in the high layer.<br>Anyway I found that could come with the "Amber" So I changed it to UFF in the low layer. Now I get some other error which does not give any understandable message. <br><br>I think I have not used commands correctly. Please someone help me to solve the problem<br><br>Here is my input file.<br><br>%chk=quick.chk<br>%mem=6MW<br>%nproc=1<br> opt=rcfc oniom(rhf/6-31g:ram1:amber) geom=connectivity<br><br>Title Card Required<br><br>0 1 0 1 0 1 0 1 0 1 0 1<br> C-CM- 0 -0.979628 -1.159218 0.000009 H<br> C-CM- 0 0.422122 -1.159218 0.000009 H<br> H-H4- 0 1.066495 -2.031924 0.000034 M H-H4 2<br> N- 0 -0.310937 1.003031 -0.000095 H<br> N-N2- 0 0.846120 0.211578 0.000009 H<br> N-N3--0.516300 0 -1.419355 0.161290 0.000000 H<br> C-CT-0.039700 0 -2.859630 0.320067
0.000068 H<br> H-H1-0.110500 0 -3.277620 -0.150672 -0.889757 M H-H1 7<br> C-CT-0.056000 0 -3.483217 -0.326921 1.232208 M H-H1 7<br> C-C-0.536600 0 -3.248651 1.791511 0.000147 M H-H1 7<br> H-HC--0.017300 0 -3.250175 -1.391678 1.241385 M<br> H-HC--0.017300 0 -3.081256 0.140223 2.131266 M<br> C-CT-0.013600 0 -4.981165 -0.140179 1.195083 M<br> O-O--0.581900 0 -2.355867 2.678364 0.000146 M<br> H-HC--0.042500 0 -5.215008 0.924407 1.186354 M<br> H-HC--0.042500 0 -5.383929 -0.607494 0.296474 M<br> C-C-0.805400 0 -5.605570 -0.788016 2.428839 M<br> O-O2--0.818800 0 -5.734708 -0.067706 3.454547 M<br> O-O2--0.818800 0 -5.947450 -1.997018 2.333810 M<br> N-N--0.415700 0 -4.667286 2.176705 0.000223 M<br> H-H-0.271900 0 -5.358580 1.538797 0.339614 M<br> C-CT--0.087500 0 -5.063971 3.480727 -0.491479 M<br> H-H1-0.096900 0
-4.580882 4.256153 0.103028 M<br> C-CT-0.298500 0 -4.660558 3.663221 -1.950786 L H-H1 22<br> C-C-0.597300 0 -6.571867 3.665676 -0.399129 L H-H1 22<br> H-HC--0.029700 0 -3.578481 3.570399 -2.043492 L<br> C-CT--0.319200 0 -5.336934 2.594335 -2.802621 L<br> C-CT--0.319200 0 -5.094761 5.044582 -2.429256 L<br> O-O--0.567900 0 -7.292069 2.741987 0.060956 L<br> H-HC-0.079100 0 -6.419114 2.686824 -2.710783 L<br> H-HC-0.079100 0 -5.048915 2.724325 -3.845812 L<br> H-HC-0.079100 0 -5.026906 1.606779 -2.460984 L<br> H-HC-0.079100 0 -4.611580 5.808946 -1.820665 L<br> H-HC-0.079100 0 -4.806645 5.175545 -3.472299 L<br> H-HC-0.079100 0 -6.176850 5.137991 -2.337278 L<br> N-N--0.516300 0 -7.186941 4.923315 -0.847381 L<br> H-H-0.293600 0 -6.651063 5.581231 -1.376513 L<br> C-CT-0.039700 0 -8.569717 5.209666 -0.522518 L<br>
H-H1-0.110500 0 -9.210774 4.437288 -0.947463 L<br> C-CT-0.056000 0 -8.783229 5.244046 0.987069 L<br> C-C-0.536600 0 -8.996294 6.558691 -1.083453 L<br> H-HC--0.017300 0 -8.518191 4.276855 1.414148 L<br> H-HC--0.017300 0 -8.154675 6.018939 1.425887 L<br> C-CT-0.013600 0 -10.233003 5.544569 1.283615 L<br> O-O--0.581900 0 -8.175766 7.258267 -1.732221 L<br> H-HC--0.042500 0 -10.498670 6.511888 0.857216 L<br> H-HC--0.042500 0 -10.862188 4.769803 0.845477 L<br> C-C-0.805400 0 -10.446796 5.578994 2.795182 L<br> O-O2--0.818800 0 -10.298521 6.688991 3.372697 L<br> O-O2--0.818800 0 -10.756343 4.494968 3.357912 L<br> N-N--0.415700 0 -10.366797 7.044417 -0.867366 L<br> H-H-0.271900 0 -10.957507 6.593282 -0.198382 L<br> C-CT--0.002400 0 -10.861782 8.176899 -1.623723 L<br> H-H1-0.097800 0 -10.239071 9.048695 -1.422967 L<br>
C-CT--0.034300 0 -10.832645 7.891714 -3.121536 L<br> C-C-0.597300 0 -12.297546 8.506169 -1.240775 L<br> H-HC-0.029500 0 -9.808555 7.685743 -3.432851 L<br> H-HC-0.029500 0 -11.459040 7.026711 -3.339479 L<br> C-CA-0.011800 0 -11.331632 9.017578 -3.995345 L<br> O-O--0.567900 0 -12.888752 7.820305 -0.366912 L<br> C-CA--0.125600 0 -11.350562 8.867789 -5.387180 L<br> C-CA--0.125600 0 -11.775340 10.211216 -3.413663 L<br> H-HA-0.133000 0 -11.005104 7.938457 -5.840061 L<br> C-CA--0.170400 0 -11.813199 9.911636 -6.197334 L<br> C-CA--0.170400 0 -12.237977 11.255063 -4.223817 L<br> H-HA-0.133000 0 -11.760602 10.327838 -2.330020 L<br> H-HA-0.143000 0 -11.827938 9.795014 -7.280977 L<br> C-CA--0.107200 0 -12.256907 11.105274 -5.615652 L<br> H-HA-0.143000 0 -12.583435 12.184395 -3.770936 L<br> H-HA-0.129700 0 -12.617104 11.917984 -6.246414 L<br>
N-N--0.347900 0 -12.993637 9.625381 -1.891714 L<br> H-H-0.274700 0 -12.550033 10.125419 -2.635473 L<br> C-CT--0.263700 0 -14.322568 10.004049 -1.455647 L<br> H-H1-0.156000 0 -15.001717 9.161287 -1.584520 L<br> C-CT--0.000700 0 -14.323143 10.410005 0.014326 L<br> C-C-0.734100 0 -14.849615 11.181352 -2.263524 L<br> H-HC-0.032700 0 -13.982173 9.572662 0.623175 L<br> H-HC-0.032700 0 -13.654477 11.258795 0.157651 L<br> C-CT-0.039000 0 -15.736543 10.800370 0.433298 L<br> O-O2--0.589400 0 -14.141789 11.688069 -3.172254 L<br> H-HC-0.028500 0 -16.078044 11.638013 -0.174841 L<br> H-HC-0.028500 0 -16.405741 9.951881 0.290683 L<br> C-CT-0.048600 0 -15.737119 11.206327 1.903273 L<br> H-H1-0.068700 0 -15.396149 10.368984 2.512121 L<br> H-H1-0.068700 0 -15.068452 12.055116 2.046597 L<br> N-N2--0.529500 0 -17.095392 11.592620 2.346300 L<br>
H-H-0.345600 0 -17.850021 11.554247 1.676106 L<br> C-CA-0.807600 0 -17.367676 11.987984 3.586642 L<br> N-N2--0.862700 0 -16.427662 12.064208 4.524438 L<br> N-N2--0.862700 0 -18.624431 12.312365 3.876888 L<br> H-H-0.447800 0 -15.474243 11.817145 4.300713 L<br> H-H-0.447800 0 -16.671555 12.368807 5.456015 L<br> H-H-0.447800 0 -19.335864 12.253370 3.162407 L<br> H-H-0.447800 0 -18.861600 12.616204 4.810447 L<br> O-OH- 0 -16.149152 11.711677 -1.989919 L<br> H-HO- 0 -16.493627 12.138214 -2.777956 L<br> C-CT- 0 -1.971529 -2.337238 0.000148 H<br> H-H1- 0 -2.312409 -2.516359 0.998454 M H-H1 97<br> H-H1- 0 -2.807007 -2.100096 -0.624865 M H-H1 97<br> N-N- 0 -1.302226 -3.541423 -0.512564 H<br> H-H- 0 -1.939344 -4.059457 -1.083284 M H-H 100<br> C-C-0.597300 0 -0.864453
-4.376461 0.615251 M H-H 100<br> C-CT--0.024900 0 -0.037047 -5.628013 0.359323 M<br> O-O--0.567900 0 -1.173802 -4.056507 1.792326 M<br> N-N--0.415700 0 0.287099 -6.301875 1.600469 M<br> H-H1-0.084300 0 0.882942 -5.339427 -0.149046 M<br> C-CT-0.211700 0 -0.840250 -6.536712 -0.565206 M<br> H-H-0.271900 0 -0.030927 -5.926491 2.471070 M<br> H-H1-0.035200 0 -0.257411 -7.428659 -0.795052 M<br> H-H1-0.035200 0 -1.768812 -6.826793 -0.073551 M<br> O-OH--0.654600 0 -1.140564 -5.838678 -1.776594 M<br> H-HO-0.427500 0 -1.646188 -6.410710 -2.358593 L H-HO 111<br> C-C-0.597300 0 1.083440 -7.537316 1.579817 M<br> C-CT--0.059700 0 1.182562 -8.399803 2.829927 L H-H2 113<br> O-O--0.567900 0 1.683197 -7.881810 0.528539 L H-H1 113<br> N-N--0.415700 0 2.011332 -9.565021 2.595383 L<br> H-H1-0.086900 0 0.179485 -8.717971 3.114015
L<br> C-CT-0.130300 0 1.787312 -7.563573 3.952701 L<br> H-H-0.271900 0 2.427990 -9.709793 1.697922 L<br> H-HC-0.018700 0 1.840278 -8.160662 4.863074 L<br> C-CT--0.320400 0 3.190484 -7.117729 3.555261 L<br> C-CT--0.043000 0 0.915074 -6.337240 4.199546 L<br> H-HC-0.088200 0 3.138271 -6.520160 2.645160 L<br> H-HC-0.088200 0 3.623208 -6.519964 4.357462 L<br> H-HC-0.088200 0 3.814318 -7.993944 3.378686 L<br> H-HC-0.023600 0 0.862007 -5.739377 3.289687 L<br> H-HC-0.023600 0 -0.088004 -6.655407 4.483633 L<br> C-CT--0.066000 0 1.519823 -5.501009 5.322319 L<br> H-HC-0.018600 0 2.522801 -5.182068 5.038746 L<br> H-HC-0.018600 0 0.896743 -4.624314 5.499167 L<br> H-HC-0.018600 0 1.572790 -6.098098 6.232692 L<br> C-C-0.536600 0 2.239625 -10.534308 3.676709 L<br> C-CT-0.039700 0 3.284848 -11.628043 3.510163 L<br>
O-O--0.581900 0 1.570859 -10.459764 4.740083 L<br> N-N--0.516300 0 3.349503 -12.471304 4.686740 L<br> H-H1-0.110500 0 4.255202 -11.160138 3.344097 L<br> C-CT-0.056000 0 2.917005 -12.439652 2.272582 L<br> H-H-0.293600 0 2.749247 -12.289694 5.465655 L<br> H-HC--0.017300 0 3.668607 -13.211525 2.107031 L<br> H-HC--0.017300 0 1.943386 -12.906989 2.420098 L<br> C-CT-0.013600 0 2.860022 -11.527101 1.070874 L<br> H-HC--0.042500 0 2.108260 -10.755186 1.235505 L<br> H-HC--0.042500 0 3.833481 -11.059722 0.922437 L<br> C-C-0.805400 0 2.491696 -12.339774 -0.168330 L<br> O-O2--0.818800 0 1.266381 -12.454522 -0.438582 L<br> O-O2--0.818800 0 3.439166 -12.838062 -0.832867 L<br> C-C-0.597300 0 4.297472 -13.593752 4.735361 L<br> C-CT--0.024900 0 4.292558 -14.543002 5.925061 L<br> O-O--0.567900 0 5.113049 -13.769784 3.793332 L<br>
N-N3--0.415700 0 5.300035 -15.573477 5.774352 L<br> H-H1-0.084300 0 3.307903 -15.004749 5.998170 L<br> C-CT-0.211700 0 4.537363 -13.715592 7.182473 L<br> H-H-0.271900 0 5.883024 -15.587765 4.961997 L<br> H-H1-0.035200 0 4.505016 -14.364945 8.057342 L<br> H-H1-0.035200 0 5.515908 -13.239521 7.119974 L<br> O-OH--0.654600 0 3.525587 -12.711534 7.296830 L<br> H-HO-0.427500 0 3.679694 -12.190672 8.088381 L<br> H-H-0.271900 0 5.412337 -16.270352 6.482698 L<br><br> 1 2 2.0 6 1.0 97 1.0<br> 2 3 1.0 5 1.0<br> 3<br> 4 5 2.0 6 1.0<br> 5<br> 6 7 1.0<br> 7 8 1.0 9 1.0 10 1.0<br> 8<br> 9 11 1.0 12 1.0 13 1.0<br> 10 14 2.0 20 1.0<br> 11<br> 12<br> 13 15 1.0 16 1.0 17 1.0<br> 14<br> 15<br> 16<br> 17 18 1.5 19 1.5<br> 18<br> 19<br> 20 21 1.0 22 1.0<br> 21<br> 22 23 1.0 24 1.0 25 1.0<br> 23<br> 24 26 1.0 27 1.0 28 1.0<br> 25 29 2.0 36 1.0<br> 26<br> 27 30 1.0 31 1.0 32 1.0<br> 28 33 1.0 34 1.0 35
1.0<br> 29<br> 30<br> 31<br> 32<br> 33<br> 34<br> 35<br> 36 37 1.0 38 1.0<br> 37<br> 38 39 1.0 40 1.0 41 1.0<br> 39<br> 40 42 1.0 43 1.0 44 1.0<br> 41 45 2.0 51 1.0<br> 42<br> 43<br> 44 46 1.0 47 1.0 48 1.0<br> 45<br> 46<br> 47<br> 48 49 1.5 50 1.5<br> 49<br> 50<br> 51 52 1.0 53 1.0<br> 52<br> 53 54 1.0 55 1.0 56 1.0<br> 54<br> 55 57 1.0 58 1.0 59 1.0<br> 56 60 2.0 71 1.0<br> 57<br> 58<br> 59 61 1.5 62 1.5<br> 60<br> 61 63 1.0 64 1.5<br> 62 65 1.5 66 1.0<br> 63<br> 64 67 1.0 68 1.5<br> 65 68 1.5 69 1.0<br> 66<br> 67<br> 68 70 1.0<br> 69<br> 70<br> 71 72 1.0 73 1.0<br> 72<br> 73 74 1.0 75 1.0 76 1.0<br> 74<br> 75 77 1.0 78 1.0 79 1.0<br> 76 80 2.0 95 1.0<br> 77<br> 78<br> 79 81 1.0 82 1.0 83 1.0<br> 80<br> 81<br> 82<br> 83 84 1.0 85 1.0 86 1.0<br> 84<br> 85<br> 86 87 1.0 88 1.5<br> 87<br> 88 89 1.5 90 1.5<br> 89 91 1.0 92 1.0<br> 90 93 1.0 94 1.0<br> 91<br> 92<br> 93<br> 94<br> 95 96 1.0<br> 96<br> 97 98 1.0 99 1.0 100 1.0<br> 98<br> 99<br> 100 101 1.0 102 1.0<br> 101<br>
102 103 1.0 104 2.0<br> 103 105 1.0 106 1.0 107 1.0<br> 104<br> 105 108 1.0 113 1.0<br> 106<br> 107 109 1.0 110 1.0 111 1.0<br> 108<br> 109<br> 110<br> 111 112 1.0<br> 112<br> 113 114 1.0 115 2.0<br> 114 116 1.0 117 1.0 118 1.0<br> 115<br> 116 119 1.0 132 1.0<br> 117<br> 118 120 1.0 121 1.0 122 1.0<br> 119<br> 120<br> 121 123 1.0 124 1.0 125 1.0<br> 122 126 1.0 127 1.0 128 1.0<br> 123<br> 124<br> 125<br> 126<br> 127<br> 128 129 1.0 130 1.0 131 1.0<br> 129<br> 130<br> 131<br> 132 133 1.0 134 2.0<br> 133 135 1.0 136 1.0 137 1.0<br> 134<br> 135 138 1.0 147 1.0<br> 136<br> 137 139 1.0 140 1.0 141 1.0<br> 138<br> 139<br> 140<br> 141 142 1.0 143 1.0 144 1.0<br> 142<br> 143<br> 144 145 1.5 146 1.5<br> 145<br> 146<br> 147 148 1.0 149 2.0<br> 148 150 1.0 151 1.0 152 1.0<br> 149<br> 150 153 1.0 158 1.0<br> 151<br> 152 154 1.0 155 1.0 156 1.0<br> 153<br> 154<br> 155<br> 156 157 1.0<br> 157<br> 158<br><br><br><br<br<br<br<br><br<br<br><br<br<br><br<br<br><br<br><br<br<br><br<br><br<br<br><br<br><br<br><br><br><br></blockquote><br><p> 
<hr size=1>Be a better Globetrotter. <a href="http://us.rd.yahoo.com/evt=48254/*http://answers.yahoo.com/dir/_ylc=X3oDMTI5MGx2aThyBF9TAzIxMTU1MDAzNTIEX3MDMzk2NTQ1MTAzBHNlYwNCQUJwaWxsYXJfTklfMzYwBHNsawNQcm9kdWN0X3F1ZXN0aW9uX3BhZ2U-?link=list&sid=396545469">Get better travel answers </a>from someone who knows.<br>Yahoo! Answers - Check it out.
--0-521775899-1184012211=:21858--
From owner-chemistry@ccl.net Mon Jul 9 21:39:01 2007
From: "Raoul E Correa raoul##berkeley.edu" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: Visualizing vibrational data
Message-Id: <-34698-070709134944-27583-9PGASXBTRy3W0blhPcqplA-#-server.ccl.net>
X-Original-From: "Raoul E Correa" <raoul.-#-.berkeley.edu>
Date: Mon, 9 Jul 2007 13:49:40 -0400
Sent to CCL by: "Raoul E Correa" [raoul+*+berkeley.edu]
Hello,
I was wondering if there is software which helps one visualize the motions of atoms along a vibrational mode, such as those described by a frequency calculation in any computational package. I run simulations on QChem but haven't found a program that will take the output and create animations of the actual vibrational mode.
Does anyone know of such a stand-alone program? Or maybe a way to convert the output into something that another program (e.g. Molekel) could use? Thanks for the help!
Raoul
From owner-chemistry@ccl.net Mon Jul 9 22:41:00 2007
From: "Thomas Jospeh alabarae.:.yahoo.com" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: what are nutlins 3a and 3b
Message-Id: <-34699-070709223646-3923-+PuBWMeW6n3BXZDYsiUzyw:+:server.ccl.net>
X-Original-From: "Thomas Jospeh" <alabarae_._yahoo.com>
Date: Mon, 9 Jul 2007 22:36:43 -0400
Sent to CCL by: "Thomas Jospeh" [alabarae[a]yahoo.com]
Hi,
what are the structural differences between nutlin 3a and nutlin3b.
they are enantiomers,
but how to differentiate them structurally,
your help is deeply appreciated.