From owner-chemistry@ccl.net Tue Aug 31 00:28:00 2010
From: "ABHISHEK SHAHI shahi.abhishek1984(~)gmail.com" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL: gaussian produces lots of imaginary frequencies
Message-Id: <-42651-100831002616-4901-dSixF4JXRo+/Qtb64HGetQ:_:server.ccl.net>
X-Original-From: ABHISHEK SHAHI <shahi.abhishek1984::gmail.com>
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Date: Tue, 31 Aug 2010 09:56:10 +0530
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Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984|a|gmail.com]
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Dear All
I have similar problem as 'Johannes Salewski ' . I am getting 3 or 4
or 5 or 6 or sometime 8 negative frequency for water complexes having 6
atoms only.Some negative Frequencies are quite larger(`2300 cm-1).How to
resolve this problem ? I have tried it for 7-8 times but got nearly same
result. I have chosen #mp2=full/aug-cc-pvtz opt=(maxcycle=100) freq=noraman
nosymm scf=(tight,vshift=150,xqc) route section with enough memory.In output
, Its showing normal termination for both optimization and frequency
calculation with several order saddle point (i.e. more negative
frequencies).I am looking for a proper suggestion.
your suggestions will appreciated
With regards;
*ABHISHEK SHAHI*
IISc bangalore-12
India
Official E-mail: shahi-$-ipc.iisc.ernet.in
CC: shahi.abhishek1984-$-gmail.com
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Dear All <br>=A0=A0=A0=A0=A0 I have similar problem as '<span class=3D"=
gI"><span class=3D"gD" style=3D"color: rgb(0, 104, 28);">Johannes Salewski =
' . I </span></span>am getting 3 or 4 or 5 or 6 or sometime 8 negative =
frequency for water complexes having 6 atoms only.Some negative Frequencies=
are quite larger(`2300 cm-1).How to resolve this problem ? I have tried it=
for 7-8 times but got nearly same result. I have chosen #mp2=3Dfull/aug-cc=
-pvtz opt=3D(maxcycle=3D100) freq=3Dnoraman nosymm scf=3D(tight,vshift=3D15=
0,xqc) route section with enough memory.In output , Its showing normal term=
ination for both optimization and frequency calculation with several order =
saddle point (i.e. more negative frequencies).I am looking for a proper sug=
gestion.<br>
<br>=A0your suggestions will appreciated <br><br><br><br><br><br clear=3D"a=
ll">With regards;<br><span style=3D"background-color: rgb(255, 255, 255);">=
=A0<font size=3D"4"><i style=3D"font-family: arial black,sans-serif;"><b><s=
pan style=3D"color: rgb(51, 51, 255);">ABHISHEK SHAHI</span></b></i></font>=
</span><br>
=A0 IISc bangalore-12<br>=A0India<br>=A0 Official E-mail: <a href=3D"mailto=
:shahi-$-ipc.iisc.ernet.in" target=3D"_blank">shahi-$-ipc.iisc.ernet.in</a><br>=
=A0 CC:=A0 <a href=3D"mailto:shahi.abhishek1984-$-gmail.com" target=3D"_blank=
">shahi.abhishek1984-$-gmail.com</a><br>
--0016364c743b0290dc048f16fb67--
From owner-chemistry@ccl.net Tue Aug 31 04:27:00 2010
From: "Johannes Salewski Johannes.Salewski]-[tu-berlin.de" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: gaussian produces lots of imaginary frequencies
Message-Id: <-42652-100831042519-20760-BkHH/lMjD7Z4aERGWsahEg**server.ccl.net>
X-Original-From: Johannes Salewski <Johannes.Salewski---tu-berlin.de>
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Date: Tue, 31 Aug 2010 10:24:53 +0200
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Sent to CCL by: Johannes Salewski [Johannes.Salewski{}tu-berlin.de]
Damian Bikiel dbikiel!=!qi.fcen.uba.ar schrieb:
> Are your structures optimized?
>
> the frequencies of a structure which is not a minimum in the potential energy
> surface is meaningless.
>
> damian
>
Yes, the structures are successfully optimised in a QM/MM geometry
optimisation with ChemShell (combining dl_poly for MM part and turbomole
for QM part). I used basis sets '6-31g hondo' for the QM atoms (types
C,N,O,S,H; the chromophore of a protein; all in 25A a water sphere).
here is an example output from optimisation.logfile:
----------------------------------------------------------------------------------------------------------------------------------------------------
[...]
Optimisation progress report:
Steps: 1 Hessian updates: 0 Function/gradient evals: 128
Function: -2481.22520513 Difference: -0.14386E-03
HDLC step and gradient:
mac MaxStep: 0.33617E-02 Target: 0.54000E-02 converged? yes
Component: 783
mac RMSStep: 0.22463E-03 Target: 0.36000E-02 converged? yes
mac *MaxGrad: 0.13337E-02 Target: 0.13500E-02 converged? yes*
Component: 783
mac RMSGrad: 0.94357E-04 Target: 0.90000E-03 converged? yes
cycle --------- converged! -------------
**************** OPTIMISED ****************
Summary of the optimisation
Function / gradient evaluations: 128
Function / gradient eval. full SCF: 128
Function / gradient eval. NO SCF: 0
Number of tried P-RFO steps: 0
Number of performed P-RFO steps: 0
Total number of tried L-BFGS steps: 127
Number of performed L-BFGS steps: 115
Number of performed microiterative L-BFGS steps: 0
Number of Hessian updates: 0
Destroying all HDLC residues
exit 1
********************************************************************************
Optimization finished sucessfully
********************************************************************************
----------------------------------------------------------------------------------------------------------------------------------------------------
Close, David M. CLOSED(~)mail.etsu.edu schrieb:
> Johannes:
> I don't know what structure you are working with, but there are some preliminary things to consider. First of all, is the frequency calculation on an optimized structure? Next, one needs to know if the imaginary frequencies have small values, say less than 300 cm-1, or they large, say like normal IR stretching frequencies of 1500 cm-1? If the imaginary frequencies are small, then you have to decide if this is normal or not. Sometimes small frequencies can be associated with rotations of something like a methyl group. So perhaps you have some more information on this?
> Regards, Dave Close.
>
The structures are optimised, see above. Values for imaginary
frequencies are up to -450 cm-1. As far as I know, there can be around
1-3 imaginary frequencies with less then 100 cm-1 resulting of the qm/mm
linking region (connection from the QM chromophore to the MM protein
environment), but I don't know, why there are at least 14.
I used (#p b3lyp/6-31g* freq=raman gfinput charge nosymm) in frequency
calculation. By the way, as you said, I could assign the most negative
frequencies to different methyl group bendings (according to gaussview).
So is this a common thing to happen?
Thanks in advance, all your help is appreciated!
Best regards,
Johannes Salewski
PS: please consider that I'm quite new to the field of CC, if you notice
stupid input errors or sth. that doesn't make sense, please tell me ;-)
From owner-chemistry@ccl.net Tue Aug 31 07:44:00 2010
From: "Rzepa, Henry h.rzepa^^^imperial.ac.uk" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL:G: Visualization of G09 output
Message-Id: <-42653-100831044834-6422-R17FX30mhgMTYdONdglFaQ ~~ server.ccl.net>
X-Original-From: "Rzepa, Henry" <h.rzepa{}imperial.ac.uk>
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Date: Tue, 31 Aug 2010 09:48:25 +0100
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Sent to CCL by: "Rzepa, Henry" [h.rzepa++imperial.ac.uk]
>You actually DO NOT HAVE to upgrade your version of GaussView just to visualization vibrations from a G-09 output. I contacted Gaussian about the inability to view vibrations generated in G-09 within non-GaussView v5.0. The solution is simple:
>
>The formatted read of the output file is particular for the white space. Within the G-09 output file, change every occurrence of
>"Atom AN" to "Atom AN"
>(note the 2 spaces between 'm' and 'A' now becomes just 1 space)
>
>Don't you just love formatted read calls?
Cannot resist pointing out that one solution to such problems was developed in 1996; it was called XML. XML is, inter alia, agnostic to "white space" and has various other advantages.
Still, Gaussian have almost squared the circle in being (almost) backward compatible whilst continuing to innovate.
PS I believe revision B.01 of G09 fixes much of this (?)
--
Professor Henry S Rzepa.
+44 (020) 7594 5774 (Voice); http://www.ch.ic.ac.uk/rzepa/ & /rzepa/blog
Dept. Chemistry, Imperial College London, SW7 2AZ, UK.
(Voracious anti-spam filter in operation for received email.
If expected reply not received, please phone/fax).
From owner-chemistry@ccl.net Tue Aug 31 08:19:00 2010
From: "Billy McCann bwm0005%%auburn.edu" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL:G: Visualization of G09 output
Message-Id: <-42654-100830192310-20483-fVkajqfTBbsybBC4IKOkeQ_+_server.ccl.net>
X-Original-From: Billy McCann <bwm0005-.-auburn.edu>
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Date: Mon, 30 Aug 2010 18:22:30 -0500
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Sent to CCL by: Billy McCann [bwm0005~~auburn.edu]
Greetings.
For visualization of Gaussian 09 calculations in Gaussian 03, Molekol
has a bash script to do this very thing available at
ftp://ftp.cscs.ch/out/molekel/molekel_5.4/convG09to03.sh
The main action of the script is a sed call:
cat $1 | sed "s/Gaussian 09/Gaussian 03/" | sed "s/Eigenvalues --
/EIGENVALUES -- /" | sed "s/Density Matrix:/DENSITY MATRIX./" | sed "s/
Atom AN/Atom AN/" > $2
which is identical to Marcel Swart's command, with some additions for
eigenvalues and density matrices. $1 is the input file; $2 will be the
output file.
Using this will enable you to even view normal modes.
Hope this helps,
Billy McCann
From owner-chemistry@ccl.net Tue Aug 31 08:54:00 2010
From: "nazanin jamshidi na.jamshidi-#-gmail.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL:G: Visualization of G09 output
Message-Id: <-42655-100831003808-8899-qohBWnZLWN1gX2CvNlL6Yw * server.ccl.net>
X-Original-From: nazanin jamshidi <na.jamshidi*o*gmail.com>
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Date: Tue, 31 Aug 2010 09:07:58 +0430
MIME-Version: 1.0
Sent to CCL by: nazanin jamshidi [na.jamshidi%a%gmail.com]
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Dear Steven
Thank you so much. I had the same problem. now I can visualize the
vibrational frequencies by changing the format.
Regards
Jamshidi
2010/8/30 Bachrach, Steven STEVEN.BACHRACH]_[Trinity.edu <
owner-chemistry- -ccl.net>
> You actually DO NOT HAVE to upgrade your version of GaussView just to
> visualization vibrations from a G-09 output. I contacted Gaussian about t=
he
> inability to view vibrations generated in G-09 within non-GaussView v5.0.
> The solution is simple:
>
>
>
> The formatted read of the output file is particular for the white space.
> Within the G-09 output file, change every occurrence of
>
> =E2=80=9CAtom AN=E2=80=9D to =E2=80=9CAtom AN=E2=80=9D
>
> (note the 2 spaces between =E2=80=98m=E2=80=99 and =E2=80=98A=E2=80=99 no=
w becomes just 1 space)
>
>
>
> Don=E2=80=99t you just love formatted read calls?
>
>
>
> Steven
>
>
>
>
>
> Steven Bachrach, Chair ph: (210)999-7379
>
> Department of Chemistry fax: (210)999-7569
>
> Trinity University
>
> 1 Trinity Place
>
> San Antonio, TX 78212
>
> steven.bachrach-x-trinity.edu
>
>
>
>
>
> *From:* owner-chemistry+steven.bachrach=3D=3Dtrinity.edu-x-ccl.net [mailt=
o:
> owner-chemistry+steven.bachrach <owner-chemistry%2Bsteven.bachrach>=3D=3D
> trinity.edu-x-ccl.net] *On Behalf Of *Thishana Singh singht_-_dut.ac.za
> *Sent:* Monday, August 30, 2010 2:49 AM
> *To:* Bachrach, Steven
>
> *Subject:* CCL:G: Visualization of G09 output
>
>
>
> Dear Abhishek
>
>
>
> What version of Gausview are you using to view G09 outputs ?
>
> You can view G09 output with Gausview Ver.5.
>
> If you have a lower version, the you need to upgrade.
>
> Hope this helps.
>
>
>
> Thishana Singh
>
> Department of Chemistry
>
> Durban University of Technology
>
> South Africa
>
>
>
> *From:* owner-chemistry+singht=3D=3Ddut.ac.za::ccl.net [mailto:
> owner-chemistry+singht <owner-chemistry%2Bsinght>=3D=3Ddut.ac.za::ccl.net=
] *On
> Behalf Of *Yi (Yves) Wang yves.wang * duke.edu
> *Sent:* 28 August 2010 08:09 PM
> *To:* Thishana Singh
> *Subject:* CCL:G: Visualization of G09 output
>
>
>
> Have you tried Gabedit and Molden?
>
>
> _________________________________________________________________________=
____
>
>
>
> Yi (Yves) Wang
>
> Department of Biochemistry
>
> Structural Biology & Biophysics Program
>
> Duke University
>
> BS: University of Science and Technology of China
>
> School of Life Sciences, National Laboratory for Physical Sciences at
> Microscale
>
> Tel: +1-919-236-3307 (Cell)
>
> +1-919-684-0235 (Lab 1)
>
> +1-919-660-1634 (Lab 2)
>
> Office: A20 LSRC / 5301 FFSC
>
> E-Mail: yves.wang[*]duke.edu
>
> Mail: Box 90317, Chemistry Department
>
>
>
> =E5=9C=A8 2010-8-28=EF=BC=8C=E4=B8=8B=E5=8D=8812:20=EF=BC=8C ABHISHEK SHA=
HI shahi.abhishek1984!^!gmail.com =E5=86=99=E9=81=93=EF=BC=9A
>
>
>
> Dear All
>
> I am facing problem in visualizing G09 output. Gaussview (not reading
> vibration),Avagadro (not reading optimisation steps),chemcraft(not readin=
g
> vibration and optimization steps).These all were suitable for G03
> output.Please suggest me that what should I do.Is <http://do.is/> there
> any free software for visualizing all results.
>
> Your suggestions will be appreciated and helpful for others
> too.........
>
>
>
>
>
>
>
>
>
> With regards;
> *ABHISHEK SHAHI*
> IISc bangalore-12
> Official E-mail: shahi()ipc.iisc.ernet.in
> CC: shahi.abhishek1984()gmail.com
>
>
>
>
> ------------------------------
>
> "This e-mail is subject to our Disclaimer, to view click
> http://www.dut.ac.za"
>
--=20
Zahra Jamshidi
Assistant Professor
Department of Physical Chemistry,
Chemistry and Chemical Engineering Research Center of Iran
P.O. Box 14335-186, Tehran, Iran.
--0016e6d2614542cf08048f1725e7
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<div>Dear Steven</div>
<div>=C2=A0</div>
<div>Thank you so much. I had the same problem. now I can visualize the vib=
rational frequencies by changing the format.<br></div>
<div>Regards</div>
<div>Jamshidi<br></div>
<div class=3D"gmail_quote">2010/8/30 Bachrach, Steven STEVEN.BACHRACH]_[Tri=
nity.edu <span dir=3D"ltr"><<a href=3D"mailto:owner-chemistry- -ccl.net">o=
wner-chemistry- -ccl.net</a>></span><br>
<blockquote style=3D"BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex=
; PADDING-LEFT: 1ex" class=3D"gmail_quote">
<div style=3D"WORD-WRAP: break-word" lang=3D"EN-US" vlink=3D"purple" link=
=3D"blue">
<div>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">You =
actually DO NOT HAVE to upgrade your version of GaussView just to visualiza=
tion vibrations from a G-09 output. I contacted Gaussian about the inabilit=
y to view vibrations generated in G-09 within non-GaussView v5.0. The solut=
ion is simple:</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">=C2=
=A0</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">The =
formatted read of the output file is particular for the white space. Within=
the G-09 output file, change every occurrence of =C2=A0</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">=E2=
=80=9CAtom=C2=A0 AN=E2=80=9D to =E2=80=9CAtom AN=E2=80=9D</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">(not=
e the 2 spaces between =E2=80=98m=E2=80=99 and =E2=80=98A=E2=80=99 now beco=
mes just 1 space)</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">=C2=
=A0</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">Don=
=E2=80=99t you just love formatted read calls?</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">=C2=
=A0</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">Stev=
en</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">=C2=
=A0</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">=C2=
=A0</span></p>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Simplified Arabic&#=
39;, 'serif'; COLOR: #1f497d; FONT-SIZE: 10pt">Steven Bachrach, Cha=
ir=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 =C2=A0=C2=A0=
=C2=A0 ph: (210)999-7379</span></p>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Simplified Arabic&#=
39;, 'serif'; COLOR: #1f497d; FONT-SIZE: 10pt">Department of Chemis=
try=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 fax: (210)999-756=
9</span></p>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Simplified Arabic&#=
39;, 'serif'; COLOR: #1f497d; FONT-SIZE: 10pt">Trinity University=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0</span></p>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Simplified Arabic&#=
39;, 'serif'; COLOR: #1f497d; FONT-SIZE: 10pt">1 Trinity Place</spa=
n></p>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Simplified Arabic&#=
39;, 'serif'; COLOR: #1f497d; FONT-SIZE: 10pt">San Antonio, TX 7821=
2</span></p>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Simplified Arabic&#=
39;, 'serif'; COLOR: #1f497d; FONT-SIZE: 10pt"><a href=3D"mailto:st=
even.bachrach-x-trinity.edu" target=3D"_blank">steven.bachrach-x-trinity.ed=
u</a></span><span style=3D"FONT-FAMILY: 'Times New Roman', 'ser=
if'; COLOR: #1f497d"></span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">=C2=
=A0</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">=C2=
=A0</span></p>
<div>
<div style=3D"BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING=
-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1p=
t solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<p class=3D"MsoNormal"><b><span style=3D"FONT-SIZE: 10pt">From:</span></b><=
span style=3D"FONT-SIZE: 10pt"> owner-chemistry+steven.bachrach=3D=3D<a hre=
f=3D"http://trinity.edu-x-ccl.net/" target=3D"_blank">trinity.edu-x-ccl.net=
</a> [mailto:<a href=3D"mailto:owner-chemistry%2Bsteven.bachrach" target=3D=
"_blank">owner-chemistry+steven.bachrach</a>=3D=3D<a href=3D"http://trinity=
.edu-x-ccl.net/" target=3D"_blank">trinity.edu-x-ccl.net</a>] <b>On Behalf =
Of </b>Thishana Singh <a href=3D"http://singht_-_dut.ac.za/" target=3D"_bla=
nk">singht_-_dut.ac.za</a><br>
<b>Sent:</b> Monday, August 30, 2010 2:49 AM<br><b>To:</b> Bachrach, Steven=
=20
<div>
<div></div>
<div class=3D"h5"><br><b>Subject:</b> CCL:G: Visualization of G09 output</d=
iv></div></span>
<p></p></p></div></div>
<div>
<div></div>
<div class=3D"h5">
<p class=3D"MsoNormal">=C2=A0</p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">Dear=
Abhishek</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">=C2=
=A0</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">What=
version of Gausview are you using to view G09 outputs ?</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">You =
can view G09 output with Gausview Ver.5.</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">If y=
ou have a lower version, the you need to upgrade.</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">Hope=
this helps.</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">=C2=
=A0</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">This=
hana Singh</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">Depa=
rtment of Chemistry</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">Durb=
an University of Technology</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">Sout=
h Africa</span></p>
<p class=3D"MsoNormal"><span style=3D"COLOR: #1f497d; FONT-SIZE: 11pt">=C2=
=A0</span></p>
<div>
<div style=3D"BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING=
-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1p=
t solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<p class=3D"MsoNormal"><b><span style=3D"FONT-SIZE: 10pt">From:</span></b><=
span style=3D"FONT-SIZE: 10pt"> owner-chemistry+singht=3D=3D<a href=3D"http=
://dut.ac.za">dut.ac.za</a>::<a href=3D"http://ccl.net/" target=3D"_blank">=
ccl.net</a> [mailto:<a href=3D"mailto:owner-chemistry%2Bsinght" target=3D"_=
blank">owner-chemistry+singht</a>=3D=3D<a href=3D"http://dut.ac.za">dut.ac.=
za</a>::<a href=3D"http://ccl.net/" target=3D"_blank">ccl.net</a>] <b>On Be=
half Of </b>Yi (Yves) Wang yves.wang * <a href=3D"http://duke.edu/" target=
=3D"_blank">duke.edu</a><br>
<b>Sent:</b> 28 August 2010 08:09 PM<br><b>To:</b> Thishana Singh<br><b>Sub=
ject:</b> CCL:G: Visualization of G09 output</span></p></div></div>
<p class=3D"MsoNormal">=C2=A0</p>
<p class=3D"MsoNormal">Have you tried Gabedit and Molden?</p>
<div>
<div>
<div>
<div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">_______________________=
______________________________________________________</span></p></div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e37a5; FONT-SIZE: 9pt">=C2=A0</span></p></div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">Yi=C2=A0(Yves) Wang</sp=
an></p></div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">Department of Biochemis=
try</span></p></div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">Structural Biology &=
; Biophysics Program</span></p></div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">Duke University</span><=
/p></div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">BS: University of Scien=
ce and Technology of China</span></p></div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">School of Life Sciences=
, National Laboratory for Physical Sciences=C2=A0at Microscale</span></p></=
div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">Tel: +1-919-236-3307 (C=
ell)</span></p></div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">=C2=A0=C2=A0=C2=A0+1-91=
9-684-0235 (Lab 1)</span></p></div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">=C2=A0=C2=A0=C2=A0+1-91=
9-660-1634 (Lab 2)</span></p></div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">Office: A20 LSRC / 5301=
FFSC</span></p></div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">E-Mail:=C2=A0<a href=3D=
"mailto:yves.wang[*]duke.edu" target=3D"_blank">yves.wang[*]duke.edu</a></s=
pan></p>
</div>
<div>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'Times New Roman'=
;, 'serif'; COLOR: #0e36a5; FONT-SIZE: 9pt">Mail: Box 90317, Chemis=
try Department</span></p></div></div></div></div></div>
<p class=3D"MsoNormal">=C2=A0</p>
<div>
<div>
<p class=3D"MsoNormal"><span lang=3D"ZH-CN">=E5=9C=A8</span> 2010-8-28<span=
lang=3D"ZH-CN">=EF=BC=8C=E4=B8=8B=E5=8D=88</span>12:20<span lang=3D"ZH-CN"=
>=EF=BC=8C</span> ABHISHEK SHAHI shahi.abhishek1984!^!<a href=3D"http://gma=
il.com/" target=3D"_blank">gmail.com</a> <span lang=3D"ZH-CN">=E5=86=99=E9=
=81=93=EF=BC=9A</span></p>
</div>
<p style=3D"MARGIN-BOTTOM: 12pt" class=3D"MsoNormal">=C2=A0</p>
<p class=3D"MsoNormal">Dear All<br><br><span style=3D"FONT-FAMILY: 'Tim=
es New Roman', 'serif'">=C2=A0=C2=A0</span> I am facing problem=
in visualizing G09 output. Gaussview (not reading vibration),Avagadro (not=
reading optimisation steps),chemcraft(not reading vibration and optimizati=
on steps).These all were suitable for G03 output.Please suggest me that wha=
t should I <a href=3D"http://do.is/" target=3D"_blank">do.Is</a> there any =
free software for visualizing all results.<br>
<br><span style=3D"FONT-FAMILY: 'Times New Roman', 'serif'"=
>=C2=A0</span>Your suggestions will be<span style=3D"FONT-FAMILY: 'Time=
s New Roman', 'serif'">=C2=A0</span> appreciated and helpful fo=
r<span style=3D"FONT-FAMILY: 'Times New Roman', 'serif'">=
=C2=A0</span> others too.........<br>
<br><br><br><br><br><br><br><br><br clear=3D"all">With regards;<br><span st=
yle=3D"FONT-FAMILY: 'Times New Roman', 'serif'; BACKGROUND:=
white">=C2=A0</span><b><i><span style=3D"BACKGROUND: white; COLOR: #3333ff=
; FONT-SIZE: 13.5pt">ABHISHEK SHAHI</span></i></b><br>
<span style=3D"FONT-FAMILY: 'Times New Roman', 'serif'">=C2=
=A0</span> IISc bangalore-12<br><span style=3D"FONT-FAMILY: 'Times New =
Roman', 'serif'">=C2=A0</span> Official E-mail: <a href=3D"mail=
to:shahi()ipc.iisc.ernet.in" target=3D"_blank">shahi()ipc.iisc.ernet.in</a>=
<br>
<span style=3D"FONT-FAMILY: 'Times New Roman', 'serif'">=C2=
=A0</span> CC:<span style=3D"FONT-FAMILY: 'Times New Roman', 's=
erif'">=C2=A0</span> <a href=3D"mailto:shahi.abhishek1984()gmail.com" t=
arget=3D"_blank">shahi.abhishek1984()gmail.com</a></p>
</div>
<p class=3D"MsoNormal">=C2=A0</p>
<p class=3D"MsoNormal"><span style=3D"FONT-FAMILY: 'MS PGothic', &#=
39;serif'">=C2=A0</span></p>
<div style=3D"TEXT-ALIGN: center" class=3D"MsoNormal" align=3D"center"><spa=
n style=3D"FONT-FAMILY: 'MS PGothic', 'serif'">
<hr align=3D"center" size=3D"2" width=3D"100%">
</span></div>
<p class=3D"MsoNormal"><span style=3D"COLOR: gray; FONT-SIZE: 10pt">"T=
his e-mail is subject to our Disclaimer, to view click <a href=3D"http://ww=
w.dut.ac.za/" target=3D"_blank">http://www.dut.ac.za</a>"</span><span =
style=3D"FONT-FAMILY: 'MS PGothic', 'serif'"></span></p>
</div></div></div></div></blockquote></div><br><br clear=3D"all"><br>-- <br=
><br>
<div>Zahra =C2=A0Jamshidi</div>
<div>Assistant =C2=A0Professor</div>
<div>Department of Physical Chemistry,=C2=A0</div>
<div><span style=3D"LINE-HEIGHT: 16px; FONT-FAMILY: 'Trebuchet MS',=
Arial, Helvetica, sans-serif; FONT-SIZE: 13px">Chemistry and Chemical Engi=
neering Research Center of Iran=C2=A0</span></div>
<div><span style=3D"LINE-HEIGHT: 16px; FONT-FAMILY: 'Trebuchet MS',=
Arial, Helvetica, sans-serif; FONT-SIZE: 13px"></span><span style=3D"LINE-=
HEIGHT: 16px; FONT-FAMILY: 'Trebuchet MS', Arial, Helvetica, sans-s=
erif; FONT-SIZE: 13px">P.O. Box 14335-186, Tehran, Iran.</span></div>
<div><span style=3D"LINE-HEIGHT: 16px; FONT-FAMILY: 'Trebuchet MS',=
Arial, Helvetica, sans-serif; FONT-SIZE: 13px"><br></span></div>
<div><span style=3D"FONT-FAMILY: Times; FONT-SIZE: medium"><pre><font color=
=3D"#800000"><br></font></pre></span></div><br>
--0016e6d2614542cf08048f1725e7--
From owner-chemistry@ccl.net Tue Aug 31 09:29:00 2010
From: "Rzepa, Henry h.rzepa[A]imperial.ac.uk" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL:G: Visualization of G09 output
Message-Id: <-42656-100831021505-21094-TiJbdoUoZ+PmcExQvaT33g(0)server.ccl.net>
X-Original-From: "Rzepa, Henry" <h.rzepa _ imperial.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 31 Aug 2010 07:14:54 +0100
Mime-Version: 1.0
Sent to CCL by: "Rzepa, Henry" [h.rzepa{}imperial.ac.uk]
>You actually DO NOT HAVE to upgrade your version of GaussView just to visualization vibrations from a G-09 output. I contacted Gaussian about the inability to view vibrations generated in G-09 within non-GaussView v5.0. The solution is simple:
>
>The formatted read of the output file is particular for the white space. Within the G-09 output file, change every occurrence of
>"Atom AN" to "Atom AN"
>(note the 2 spaces between 'm' and 'A' now becomes just 1 space)
>
>Don't you just love formatted read calls?
Cannot resist pointing out that one solution to such problems was developed in 1996; it was called XML. XML is, inter alia, agnostic to "white space" and has various other advantages.
Still, Gaussian have almost squared the circle in being (almost) backward compatible whilst continuing to innovate.
PS I believe revision B.01 of G09 fixes much of this (?)
--
+44 (020) 7594 5774 (Voice); Blog: http://www.ch.ic.ac.uk/rzepa/blog/
Dept. Chemistry, Imperial College London, SW7 2AZ, UK.
(Voracious anti-spam filter in operation for received email.
If expected reply not received, please phone/fax).
From owner-chemistry@ccl.net Tue Aug 31 10:04:00 2010
From: "Mahmoud A. A. Ibrahim m.ibrahim_._compchem.net" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: gaussian produces lots of imaginary frequencies
Message-Id: <-42657-100831033237-7936-22G/Rq5f0xbq5PJ/13cigw%server.ccl.net>
X-Original-From: "Mahmoud A. A. Ibrahim" <m.ibrahim]_[compchem.net>
Content-Type: multipart/alternative; boundary=0015175ca7f65602d1048f1995ba
Date: Tue, 31 Aug 2010 08:32:29 +0100
MIME-Version: 1.0
Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim~!~compchem.net]
--0015175ca7f65602d1048f1995ba
Content-Type: text/plain; charset=ISO-8859-1
Dear Abhishek and Johannes
I am afraid, you have done frequency calculations at level different from
the level you have optimized your molecule at. In other words,
frequency calculations must be done at the same level of optimization,
otherwise it will be meaningless.
If it is not the case, we would love to have a look on your molecule.
Sincerely;
M. Ibrahim
On Tue, Aug 31, 2010 at 5:26 AM, ABHISHEK SHAHI shahi.abhishek1984(~)
gmail.com <owner-chemistry%%ccl.net> wrote:
> Dear All
> I have similar problem as 'Johannes Salewski ' . I am getting 3 or 4
> or 5 or 6 or sometime 8 negative frequency for water complexes having 6
> atoms only.Some negative Frequencies are quite larger(`2300 cm-1).How to
> resolve this problem ? I have tried it for 7-8 times but got nearly same
> result. I have chosen #mp2=full/aug-cc-pvtz opt=(maxcycle=100) freq=noraman
> nosymm scf=(tight,vshift=150,xqc) route section with enough memory.In output
> , Its showing normal termination for both optimization and frequency
> calculation with several order saddle point (i.e. more negative
> frequencies).I am looking for a proper suggestion.
>
> your suggestions will appreciated
>
>
>
>
>
> With regards;
> *ABHISHEK SHAHI*
> IISc bangalore-12
> India
> Official E-mail: shahi|*|ipc.iisc.ernet.in<shahi%7C*%7Cipc.iisc.ernet.in>
> CC: shahi.abhishek1984|*|gmail.com <shahi.abhishek1984%7C*%7Cgmail.com>
>
--
Mahmoud A. A. Ibrahim
Current Address
7.05, School of Chemistry,
The University of Manchester,
Oxford Road, Manchester, M13 9PL,
United Kingdom.
Home Address
Chemistry Department,
Faculty of Science,
Minia University,
Minia 61519,
Egypt.
Contact Information
Email: m.ibrahim%%compchem.net
Website: www.compchem.net
Fax No.: +20862342601
--0015175ca7f65602d1048f1995ba
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Dear Abhishek and Johannes<div>I am afraid, you have done frequency calcula=
tions at level different from the level you have optimized your molecule at=
. In other words, frequency=A0calculations must be done at the same level o=
f optimization, otherwise it will be meaningless.</div>
<div>If it is not the case, we would love to have a look on your molecule.<=
/div><div>Sincerely;</div><div>M. Ibrahim</div><div><br><div class=3D"gmail=
_quote">On Tue, Aug 31, 2010 at 5:26 AM, ABHISHEK SHAHI shahi.abhishek1984(=
~)<a href=3D"http://gmail.com">gmail.com</a> <span dir=3D"ltr"><<a href=
=3D"mailto:owner-chemistry%%ccl.net">owner-chemistry%%ccl.net</a>></span> =
wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;">Dear All <br>=A0=A0=A0=A0=A0 I have similar=
problem as '<span><span style=3D"color:rgb(0, 104, 28)">Johannes Salew=
ski ' . I </span></span>am getting 3 or 4 or 5 or 6 or sometime 8 negat=
ive frequency for water complexes having 6 atoms only.Some negative Frequen=
cies are quite larger(`2300 cm-1).How to resolve this problem ? I have trie=
d it for 7-8 times but got nearly same result. I have chosen #mp2=3Dfull/au=
g-cc-pvtz opt=3D(maxcycle=3D100) freq=3Dnoraman nosymm scf=3D(tight,vshift=
=3D150,xqc) route section with enough memory.In output , Its showing normal=
termination for both optimization and frequency calculation with several o=
rder saddle point (i.e. more negative frequencies).I am looking for a prope=
r suggestion.<br>
<br>=A0your suggestions will appreciated <br><br><br><br><br><br clear=3D"a=
ll">With regards;<br><span style=3D"background-color:rgb(255, 255, 255)">=
=A0<font size=3D"4"><i style=3D"font-family:arial black,sans-serif"><b><spa=
n style=3D"color:rgb(51, 51, 255)">ABHISHEK SHAHI</span></b></i></font></sp=
an><br>
=A0 IISc bangalore-12<br>=A0India<br>=A0 Official E-mail: <a href=3D"mailto=
:shahi%7C*%7Cipc.iisc.ernet.in" target=3D"_blank">shahi|*|ipc.iisc.ernet.in=
</a><br>=A0 CC:=A0 <a href=3D"mailto:shahi.abhishek1984%7C*%7Cgmail.com" ta=
rget=3D"_blank">shahi.abhishek1984|*|gmail.com</a><br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>=A0 =A0 =A0 =A0 =A0 =A0=
=A0 =A0 =A0 Mahmoud A. A. Ibrahim=A0 =A0 =A0 =A0=A0 <br>=A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Current Address<br>=A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0=A0 7.05, School of Chemistry,<br>=A0 =A0 =A0 =A0 =A0 =A0 =A0 The Un=
iversity of Manchester,<br>
=A0 =A0 =A0 =A0=A0 Oxford Road, Manchester, M13 9PL, <br>=A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 United Kingdom.<br><br>=A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 Home Address<br>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
=A0 Chemistry Department,<br>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Fa=
culty of Science,<br>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia =
University,<br>
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Minia 61519,<br>=A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Egypt. <br><br>=
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Contact Information<br>=A0 =A0 =
=A0 =A0 =A0=A0 Email: <a href=3D"mailto:m.ibrahim%%compchem.net">m.ibrahim%%c=
ompchem.net</a><br>
=A0 =A0 =A0 =A0 =A0 =A0 =A0 Website: <a href=3D"http://www.compchem.net">ww=
w.compchem.net</a><br>=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Fax No.: +2086=
2342601<br>
</div>
--0015175ca7f65602d1048f1995ba--
From owner-chemistry@ccl.net Tue Aug 31 11:56:00 2010
From: "lamees hegazy lameesshams * yahoo.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: MDS and LES question
Message-Id: <-42658-100831115433-6383-n1MHFmEV2EcKQBGe4PDqaA_._server.ccl.net>
X-Original-From: lamees hegazy <lameesshams%a%yahoo.com>
Content-Type: multipart/alternative; boundary="0-846529322-1283270062=:34239"
Date: Tue, 31 Aug 2010 08:54:22 -0700 (PDT)
MIME-Version: 1.0
Sent to CCL by: lamees hegazy [lameesshams * yahoo.com]
--0-846529322-1283270062=:34239
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable
Dear CCL,=20
I have been studying the probability of presence of oxygen binding pocket i=
n a dioxygenase enzyme . The pocket has not been verified by the crystal st=
ructure. I used MD simulation and LES in this study. The oxygen copy/copies=
remained within 1A from the binding pocket for 50-100 ps, then started lea=
king out . How long should the oxygen remain in the=A0 proposed binding poc=
ket to verify its presence?. All the literature I have read so far were stu=
dying the gas diffusion pathways not the gas biding pocket.
Other Two questions related to MD analysis:
1- I need to plot the probabilty of oxygen molecules within 1A of the pocke=
t against time.=A0 How should I calculate the probability?
2- How should I locate the center of mass of the oxygen copies?
Thank you,
Lamees=20
=0A=0A=0A
--0-846529322-1283270062=:34239
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable
<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;">Dear CCL, <br><br>I have been studying the pr=
obability of presence of oxygen binding pocket in a dioxygenase enzyme . Th=
e pocket has not been verified by the crystal structure. I used MD simulati=
on and LES in this study. The oxygen copy/copies remained within 1A from th=
e binding pocket for 50-100 ps, then started leaking out . How long should =
the oxygen remain in the proposed binding pocket to verify its presen=
ce?. All the literature I have read so far were studying the gas diffusion =
pathways not the gas biding pocket.<br><br>Other Two questions related to M=
D analysis:<br><br>1- I need to plot the probabilty of oxygen molecules wit=
hin 1A of the pocket against time. How should I calculate the probabi=
lity?<br><br>2- How should I locate the center of mass of the oxygen copies=
?<br><br><br>Thank you,<br>Lamees <br><br><br></td></tr></table><br>=0A=0A=
=0A=0A=0A=0A=0A=0A
--0-846529322-1283270062=:34239--