From owner-chemistry@ccl.net Tue Aug 31 00:28:00 2010 From: "ABHISHEK SHAHI shahi.abhishek1984(~)gmail.com" 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 Content-Type: multipart/alternative; boundary=0016364c743b0290dc048f16fb67 Date: Tue, 31 Aug 2010 09:56:10 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984|a|gmail.com] --0016364c743b0290dc048f16fb67 Content-Type: text/plain; charset=ISO-8859-1 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 --0016364c743b0290dc048f16fb67 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All
=A0=A0=A0=A0=A0 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=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.

=A0your suggestions will appreciated





With regards;
= =A0ABHISHEK SHAHI=
=A0 IISc bangalore-12
=A0India
=A0 Official E-mail: shahi-$-ipc.iisc.ernet.in
= =A0 CC:=A0 shahi.abhishek1984-$-gmail.com
--0016364c743b0290dc048f16fb67-- From owner-chemistry@ccl.net Tue Aug 31 04:27:00 2010 From: "Johannes Salewski Johannes.Salewski]-[tu-berlin.de" 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 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 31 Aug 2010 10:24:53 +0200 MIME-Version: 1.0 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" To: CCL Subject: CCL:G: Visualization of G09 output Message-Id: <-42653-100831044834-6422-R17FX30mhgMTYdONdglFaQ ~~ server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Tue, 31 Aug 2010 09:48:25 +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 (?) -- 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" To: CCL Subject: CCL:G: Visualization of G09 output Message-Id: <-42654-100830192310-20483-fVkajqfTBbsybBC4IKOkeQ_+_server.ccl.net> X-Original-From: Billy McCann Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 30 Aug 2010 18:22:30 -0500 MIME-Version: 1.0 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" To: CCL Subject: CCL:G: Visualization of G09 output Message-Id: <-42655-100831003808-8899-qohBWnZLWN1gX2CvNlL6Yw * server.ccl.net> X-Original-From: nazanin jamshidi Content-Type: multipart/alternative; boundary=0016e6d2614542cf08048f1725e7 Date: Tue, 31 Aug 2010 09:07:58 +0430 MIME-Version: 1.0 Sent to CCL by: nazanin jamshidi [na.jamshidi%a%gmail.com] --0016e6d2614542cf08048f1725e7 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable 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 =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 =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 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 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Steven
=C2=A0
Thank you so much. I had the same problem. now I can visualize the vib= rational frequencies by changing the format.
Regards
Jamshidi
2010/8/30 Bachrach, Steven STEVEN.BACHRACH]_[Tri= nity.edu <o= wner-chemistry- -ccl.net>

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:

=C2= =A0

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

=E2= =80=9CAtom=C2=A0 AN=E2=80=9D to =E2=80=9CAtom AN=E2=80=9D

(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)

=C2= =A0

Don= =E2=80=99t you just love formatted read calls?

=C2= =A0

Stev= en

=C2= =A0

=C2= =A0

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

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

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

1 Trinity Place

San Antonio, TX 7821= 2

steven.bachrach-x-trinity.ed= u

=C2= =A0

=C2= =A0

From:<= span style=3D"FONT-SIZE: 10pt"> owner-chemistry+steven.bachrach=3D=3Dtrinity.edu-x-ccl.net= [mailto:owner-chemistry+steven.bachrach=3D=3Dtrinity.edu-x-ccl.net] On Behalf = Of Thishana Singh singht_-_dut.ac.za
Sent: Monday, August 30, 2010 2:49 AM
To: Bachrach, Steven= =20


Subject: CCL:G: Visualization of G09 output

=C2=A0

Dear= Abhishek

=C2= =A0

What= version of Gausview are you using to view G09 outputs ?

You = can view G09 output with Gausview Ver.5.

If y= ou have a lower version, the you need to upgrade.

Hope= this helps.

=C2= =A0

This= hana Singh

Depa= rtment of Chemistry

Durb= an University of Technology

Sout= h Africa

=C2= =A0

From:<= span style=3D"FONT-SIZE: 10pt"> owner-chemistry+singht=3D=3Ddut.ac.za::= ccl.net [mailto:owner-chemistry+singht=3D=3Ddut.ac.= za::ccl.net] On Be= half Of Yi (Yves) Wang yves.wang * duke.edu
Sent: 28 August 2010 08:09 PM
To: Thishana Singh
Sub= ject: CCL:G: Visualization of G09 output

=C2=A0

Have you tried Gabedit and Molden?

_______________________= ______________________________________________________

=C2=A0

Yi=C2=A0(Yves) Wang

Department of Biochemis= try

Structural Biology &= ; Biophysics Program

Duke University<= /p>

BS: University of Scien= ce and Technology of China

School of Life Sciences= , National Laboratory for Physical Sciences=C2=A0at Microscale

Tel: +1-919-236-3307 (C= ell)

=C2=A0=C2=A0=C2=A0+1-91= 9-684-0235 (Lab 1)

=C2=A0=C2=A0=C2=A0+1-91= 9-660-1634 (Lab 2)

Office: A20 LSRC / 5301= FFSC

E-Mail:=C2=A0yves.wang[*]duke.edu

Mail: Box 90317, Chemis= try Department

=C2=A0

=E5=9C=A8 2010-8-28=EF=BC=8C=E4=B8=8B=E5=8D=8812:20=EF=BC=8C ABHISHEK SHAHI shahi.abhishek1984!^!gmail.com =E5=86=99=E9= =81=93=EF=BC=9A

=C2=A0

Dear All

=C2=A0=C2=A0 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 do.Is there any = free software for visualizing all results.

=C2=A0Your suggestions will be=C2=A0 appreciated and helpful fo= r= =C2=A0 others too.........









With regards;
=C2=A0ABHISHEK SHAHI
=C2= =A0 IISc bangalore-12
=C2=A0 Official E-mail: shahi()ipc.iisc.ernet.in=
=C2= =A0 CC:=C2=A0 shahi.abhishek1984()gmail.com

=C2=A0

=C2=A0

"T= his e-mail is subject to our Disclaimer, to view click http://www.dut.ac.za"




--
Zahra =C2=A0Jamshidi
Assistant =C2=A0Professor
Department of Physical Chemistry,=C2=A0
Chemistry and Chemical Engi= neering Research Center of Iran=C2=A0
P.O. Box 14335-186, Tehran, Iran.



--0016e6d2614542cf08048f1725e7-- From owner-chemistry@ccl.net Tue Aug 31 09:29:00 2010 From: "Rzepa, Henry h.rzepa[A]imperial.ac.uk" 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" 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" 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" 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 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 > CC: shahi.abhishek1984|*|gmail.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
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.
If it is not the case, we would love to have a look on your molecule.<= /div>
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
=A0=A0=A0=A0=A0 I have similar= problem as 'Johannes Salew= ski ' . I 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.

=A0your suggestions will appreciated





With regards;
= =A0ABHISHEK SHAHI
=A0 IISc bangalore-12
=A0India
=A0 Official E-mail: shahi|*|ipc.iisc.ernet.in=
=A0 CC:=A0 shahi.abhishek1984|*|gmail.com



--
=A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 Mahmoud A. A. Ibrahim=A0 =A0 =A0 =A0=A0
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0=A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 The Un= iversity of Manchester,
=A0 =A0 =A0 =A0=A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Fa= culty of Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia = University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Contact Information
=A0 =A0 = =A0 =A0 =A0=A0 Email: m.ibrahim%%c= ompchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Fax No.: +2086= 2342601
--0015175ca7f65602d1048f1995ba-- From owner-chemistry@ccl.net Tue Aug 31 11:56:00 2010 From: "lamees hegazy lameesshams * yahoo.com" To: CCL Subject: CCL: MDS and LES question Message-Id: <-42658-100831115433-6383-n1MHFmEV2EcKQBGe4PDqaA_._server.ccl.net> X-Original-From: lamees hegazy 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
Dear CCL,

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.

Other Two questions related to M= D analysis:

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?

2- How should I locate the center of mass of the oxygen copies= ?


Thank you,
Lamees



=0A=0A= =0A=0A=0A=0A=0A=0A --0-846529322-1283270062=:34239--