From owner-chemistry@ccl.net Fri Jul 20 00:27:00 2012 From: "Hao-Bo Guo guohaobo#,#gmail.com" To: CCL Subject: CCL: how to align the protein in popc membrane using NAMD Message-Id: <-47247-120720002615-5145-CE/tPBtwoDgvFNSwERF6Pw!^!server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/alternative; boundary=20cf3079bdda4913c304c53b4bd4 Date: Fri, 20 Jul 2012 00:26:03 -0400 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo**gmail.com] --20cf3079bdda4913c304c53b4bd4 Content-Type: text/plain; charset=ISO-8859-1 I also suggest the membrane tutorial from namd: http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/mem-tutorial.pdf Hao-Bo Guo Center for Molecular Biophysics Oak Ridge National Laboratory On Thu, Jul 19, 2012 at 1:06 PM, Venable, Richard (NIH/NHLBI) E venabler(-) nhlbi.nih.gov wrote: > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler*nhlbi.nih.gov > ] > > I suggest a visit to www.charmm-gui.org which features a membrane system > builder, and exports files for both CHARMM and NAMD packages. > > -- > Rick Venable 5635 FL/T906 > Membrane Biophysics Section > NIH/NHLBI Lab. of Computational Biology > Bethesda, MD 20892-9314 U.S.A. > (301) 496-1905 venabler AT nhlbi*nih*gov > > > > From: "Barry Hardy barry.hardy*o*vtxmail.ch" > > Reply-To: CCL Subscribers > > Date: Thu, 19 Jul 2012 05:23:40 -0400 > To: "Venable, Richard (NIH/NHLBI) [E]" venabler..nhlbi.nih.gov>> > Subject: CCL: how to align the protein in popc membrane using NAMD > > > > Hi all, > > please guide me how to align the protein in popc membrane using NAMD if we > know that the residue like 8 to 31 , 56 to 72 , 91 to 121 etc how we can > embed these residue in membrane while other remain outside the membrane how > we can fix these residue in the membrane. please guide me if anyone know > about it. > i will appreciate. > > Regards, > > Maria Saeed > > > > > > > --20cf3079bdda4913c304c53b4bd4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
I also suggest the membrane tutorial from namd:
http= ://www.ks.uiuc.edu/Training/Tutorials/science/membrane/mem-tutorial.pdf=

Hao-Bo Guo
Center for Molecular Biophysics
Oak Ridge National Laboratory

On Thu, Jul 19, 2012 at 1:06 PM, Venable, Richard (NIH/NHLBI) E venable= r(-)nhlbi.nih.gov &l= t;owner-chemis= try/a\ccl.net> wrote:

Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler*nhlbi.nih.gov]

I suggest a visit to =A0www.charmm-gui.org which features a membrane system builder, and e= xports files for both CHARMM and NAMD packages.

--
Rick Venable =A0 =A0 5635 FL/T906
Membrane Biophysics Section
NIH/NHLBI Lab. of Computational Biology
Bethesda, MD =A020892-9314 =A0 U.S.A.
(301) 496-1905<= /a>=A0 =A0venabler AT nhlbi*nih*gov


> From: "Barry Hardy barry.hardy*o*vtxmail.ch" <owner-chemistry..ccl.net<mailto:owner-chemistry..ccl.net>>
Reply-To: CCL Subscribers <chemistry..ccl.net<mailto:che= mistry..ccl.net>>
Date: Thu, 19 Jul 2012 05:23:40 -0400
To: "Venable, Richard (NIH/NHLBI) [E]" <venabler..nhlbi.nih.gov<mailto:venabler..nhlbi.nih.gov>>
Subject: CCL: how to align the protein in popc membrane using NAMD



Hi all,

please guide me how to align the protein in popc membrane using NAMD if we = know that the residue like 8 to 31 , 56 to 72 =A0, 91 to =A0121 etc how we = can embed these residue in membrane while other remain outside the membrane= how we can fix these residue in the membrane. please guide me if anyone kn= ow about it.
i will appreciate.

Regards,

Maria Saeed



<http://sites.google.com/site/zaheerqasmi/groupmember> <http://zaheer%20qasmi&g= t;



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--20cf3079bdda4913c304c53b4bd4-- From owner-chemistry@ccl.net Fri Jul 20 03:45:00 2012 From: "Peter Bladon p.bladon- -strath.ac.uk" To: CCL Subject: CCL: 3D molecular modelling software Message-Id: <-47248-120719213842-2268-D0Zzr/bwwz9h76NcKWe/3A(-)server.ccl.net> X-Original-From: Peter Bladon Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 Jul 2012 02:37:24 +0100 MIME-Version: 1.0 Sent to CCL by: Peter Bladon [p.bladon]-[strath.ac.uk] Dear Gustavo L. C. Moura, Yes, the Interprobe Software, that includes INTERCHEM that does have 3D facilities. INTERCHEM runs under Windows (2000,xp, vista, and 7). The 3D faciities work under Windows Vista and 7 machines equipped with Nvidia graphics cards and IR emitters. A monitor with 120 Hz refresh capabiities (selected from a list on Nvidia's site) ia also needed The program is available under an open source license and is downloadable (FREE) by FTP from www.interprobe.co.uk (81.138.7.60). More details of the licensing are on http://www.interprobe.co.uk/inter/interprobe.html. The program 3D aspects of INTERCHEM do NOT work on HP ENVY 17 systems although other parts function normally. ENVY machines are equiped with VGA graphics, and although they will provide 3D with Movies through the Blu-Ray disc reader, they fail with the OpenGL Quad buffering systems. The glasses provided with the ENVY do not work with Nvidia 3D systems and vice versa (glasses working on different IR frequencies?). The Interprobe Software is featured by the book "Molecular Modelling; Computational Chemistry Demystified" (Bladon, Gorton, and Hammond, published by Royal Society of Chemistry. ISBN 978-1-84973-352-6), which includes the software on discs. I hope this helps Peter Bladon Dr Peter Bladon Interprobe Chemical Services Gallowhill House, Larch Avenue Lenzie, Kirkintilloch Glasgow G66 4HX Scotland, UK Telephone: 0141-578-1109 Facsimile: 0141-776-7712 URL: www.interprobe.co.uk/inter/interprobe.html ________________________________________ Dr Peter Bladon Interprobe Chemical Services Gallowhill House, Larch Avenue Lenzie, Kirkintilloch Glasgow G66 4HX Scotland, UK Telephone: 0141-578-1109 Facsimile: 0141-776-7712 URL: www.interprobe.co.uk/inter/interprobe.html ________________________________________ > From: owner-chemistry+cbas25==strath.ac.uk(~)ccl.net [owner-chemistry+cbas25==strath.ac.uk(~)ccl.net] On Behalf Of Gustavo L.C. Moura gustavo.moura]*[ufpe.br [owner-chemistry(~)ccl.net] Sent: Wednesday, July 18, 2012 10:01 PM To: Bladon, Peter Subject: CCL: 3D molecular modelling software Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura.:.ufpe.br] Dear CCL Readers, Would any of you know a molecular modelling software in 3D which can be used to visualize molecules, conformational analysis, molecular dynamics trajectories, docking, etc, using stereo glasses compatible with either NVIDIA 3D Vision or Blu-Ray? Thank you very much in advance. Sincerely yours, Gustavo L.C. Mourahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Jul 20 07:41:00 2012 From: "may abdelghani may01dz^^^yahoo.fr" To: CCL Subject: CCL: Re : CCL: positive energy of the frontier orbital Message-Id: <-47249-120720073425-22382-+Py7MxAF1EMDx/g+3f8dnQ,+,server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="-1578982885-754566828-1342784056=:38443" Date: Fri, 20 Jul 2012 12:34:16 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz]|[yahoo.fr] ---1578982885-754566828-1342784056=:38443 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCLers =0A=0AAny molecule has a height tendency to coordinate to other moiety=0Ato= form a new more stable compound=0Ais an unstable molecule. And I see that = the most compound that have a positive=0AHOMO's energy have this behavior. = This is what I mean by an unstable=0Acompound.=0A=0A --- En date de=A0: Jeu 19.7.12, Frank Jensen frj[]chem.au.dk a =E9crit=A0: De: Frank Jensen frj[]chem.au.dk Objet: CCL: positive energy of the frontier orbital =C0: "Abdelghani, May " Date: Jeudi 19 juillet 2012, 1h56 Sent to CCL by: Frank Jensen [frj#,#chem.au.dk] A positiv HOMO energy means that the total energy can be lowered by removin= g some of the electron density. A free electron has an 'orbital' energy of = zero, thus in a sufficiently flexible basis set, the electron density in th= e HOMO can be transfered to a free electron state, and give a lower energy = state. This is common when using DFT for anions, where transfer of a fraction of t= he HOMO density to an unbound electron 'orbital' gives a lower energy state= . Note that a 'sufficiently flexible basis set' is not just your favorite bas= is set augmented with diffuse functions, it must contain diffuse functions = with exponents in ~10^-4 or less range. Frank Citat af "may abdelghani may01dz[*]yahoo.fr" : >=20 >=20 > Dear CCL'ers > If=A0 the frontier orbital > (HOMO's) energy of a compound have a positive value, is this a conclusive= evidence > that this compound is a unstable > one. > A.May >=20 >=20 Frank Jensen Assoc. Prof. Dept. of Chemistry Aarhus University http://old.chem.au.dk/~frj -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubscribe:=A0 =A0=A0=A0http://www.ccl.net/chemistry/sub_unsub.s= htmlJob: http://www.ccl.net/jobsConferences: http://server.ccl.net/chemistry/an= nouncements/conferences/=A0 =A0=A0=A0http://www.ccl.net/spammers.txt---1578982885-754566828-1342784056=:38443 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCLers

=0A=0A

Any molecule has a height tendency to coordinate to other moiety=0Ato = form a new more stable compound=0Ais an unstable molecule. And I see that the most compou= nd that have a positive=0AHOMO's energy have this behavior. This is what I mean by an unstable=0Acompound= .

=0A=0A

--- En date de : Jeu 19.7.12, = Frank Jensen frj[]chem.au.dk <owner-chemistry|a|ccl.net> a = =E9crit :

De: Frank Jensen frj[]chem.a= u.dk <owner-chemistry|a|ccl.net>
Objet: CCL: positive energy of the = frontier orbital
=C0: "Abdelghani, May " <may01dz|a|yahoo.fr>= ;
Date: Jeudi 19 juillet 2012, 1h56


= Sent to CCL by: Frank Jensen [frj#,#chem.au.dk]
A positiv HOMO energy me= ans that the total energy can be lowered by removing some of the electron d= ensity. A free electron has an 'orbital' energy of zero, thus in a sufficie= ntly flexible basis set, the electron density in the HOMO can be transfered= to a free electron state, and give a lower energy state.

This is co= mmon when using DFT for anions, where transfer of a fraction of the HOMO de= nsity to an unbound electron 'orbital' gives a lower energy state.

Note that a 'sufficiently fle= xible basis set' is not just your favorite basis set augmented with diffuse= functions, it must contain diffuse functions with exponents in ~10^-4 or l= ess range.

Frank




Citat af "may abdelghani may01dz= [*]yahoo.fr" <owner-chemistry/a\ccl.net>:

>
>
&g= t; Dear CCL'ers
> If  the frontier orbital
> (HOMO's) ener= gy of a compound have a positive value, is this a conclusive evidence
&g= t; that this compound is a unstable
> one.
> A.May
>
= >



Frank Jensen
Assoc. Prof.
Dept. of Chemistry
= Aarhus University
http://old.chem.au.dk/~frj



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---1578982885-754566828-1342784056=:38443-- From owner-chemistry@ccl.net Fri Jul 20 09:22:00 2012 From: "Cina Foroutan-Nejad canyslopus#%#yahoo.co.uk" To: CCL Subject: CCL: C84 Fullerenes Message-Id: <-47250-120720091539-22585-bnBpSQAMm6G0KeDIeSZD9Q#%#server.ccl.net> X-Original-From: "Cina Foroutan-Nejad" Date: Fri, 20 Jul 2012 09:15:38 -0400 Sent to CCL by: "Cina Foroutan-Nejad" [canyslopus%a%yahoo.co.uk] Dear CCLers; I would be really thankful if anyone could provide me a Z-matrix of [84] fullerene with D2d point group (the lowest energy isomer of C84). In addition, I would be absolutely grateful if someone can also provide me the total electronic energy of C84 fullerenes at B3LYP/6-31G(d) computational level. Thank you for your time and consideration in advance. Respectfully yours, Cina Foroutan-Nejad From owner-chemistry@ccl.net Fri Jul 20 10:29:00 2012 From: "M Shabbir shabbir193rb{:}gmail.com" To: CCL Subject: CCL: Highlighting some part of a molecule Message-Id: <-47251-120720102556-31755-6EjN11qAwBmu2aob/t292A[A]server.ccl.net> X-Original-From: "M Shabbir" Date: Fri, 20 Jul 2012 10:25:54 -0400 Sent to CCL by: "M Shabbir" [shabbir193rb~~gmail.com] Dear CCL colleagues, How is it possible by using (GuessView or Macmolepro etc.) to highlight some specific atoms in a molecule? Thanks in advance! regards, Dr.Shabbir From owner-chemistry@ccl.net Fri Jul 20 11:16:00 2012 From: "Wei Deng cinf.david.deng|gmail.com" To: CCL Subject: CCL: Program Announcement "Hunting for Hidden Treasures: Chemical Informati Message-Id: <-47252-120717133142-341-NKtIkJ/vAJf8/JPlUAeGcQ-*-server.ccl.net> X-Original-From: "Wei Deng" Date: Tue, 17 Jul 2012 13:31:40 -0400 Sent to CCL by: "Wei Deng" [cinf.david.deng!=!gmail.com] Dear everyone, The full program of Hunting for Hidden Treasures: Chemical Information in Patents and Other Documents at the Philadelphia ACS meeting 2012 is now available online. We have collected over 20 abstracts, and will have three half-day sessions. Hope to see you in Philly! Detailed agenda at: http://www.chemaxon.com/events/symposium-on-244th-acs-meeting-hunting-for-hidden-treasures-chemical-information-in-patents-and-other-documents/ Best regards Wei Deng (David) From owner-chemistry@ccl.net Fri Jul 20 11:51:01 2012 From: "Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com" To: CCL Subject: CCL:G: Inquery about Gaussian Jobs Commond Message-Id: <-47253-120720064258-19983-/zmOHwQPTyeaRAKpxtYi7A(~)server.ccl.net> X-Original-From: " Bhupesh Kumar Mishra" Date: Fri, 20 Jul 2012 06:42:56 -0400 Sent to CCL by: " Bhupesh Kumar Mishra" [bhupesh_chem]*[rediffmail.com] Dear All, I am researcher in field of computational chemistry. I want to optimized Au and Ag clustes using B3LYP/LANL2DZ basis set using Gaussian09. But it failed indicating an error of internal coordinates systems. I have tried many times with SCF=QC or opt(scf=maxcycles=300) but i could not get optimized geometriesand also NBO analysis. It will be very much fruitful if any one suggest me and specific commonds for route section in input file. Your response is eagerly awaited. With best regards Bhupesh Kr Mishra bhupesh_chem/a\rediffmail.com From owner-chemistry@ccl.net Fri Jul 20 12:52:01 2012 From: "Billy McCann bwm0005]*[tigermail.auburn.edu" To: CCL Subject: CCL: Highlighting some part of a molecule Message-Id: <-47254-120720115742-23525-Mnthp+TvdBmDsvvzrnyGOQ/a\server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 Jul 2012 15:57:27 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005]-[tigermail.auburn.edu] Hello Dr. Shabbir, In Gaussview, you can select Edit > Atom list. From there, you'll get the atom list for which there is a "highlight" column. Just select the atom(s) you'd like to highlight and click on the corresponding cell. I don't think that the highlight color is configurable. I'm using GaussView5 for Windows. Hope that helps. +++++++++++++++++++++++++ Billy Wayne McCann Ph.D. Candidate Orlando Acevedo Reseach Auburn University, Alabama Office # = 334.844.6948 bwayne on irc.freenode.net +++++++++++++++++++++++++ -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu*ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu*ccl.net] On Behalf Of M Shabbir shabbir193rb{:}gmail.com Sent: Friday, July 20, 2012 9:26 AM To: Billy McCann Subject: CCL: Highlighting some part of a molecule Sent to CCL by: "M Shabbir" [shabbir193rb~~gmail.com] Dear CCL colleagues, How is it possible by using (GuessView or Macmolepro etc.) to highlight some specific atoms in a molecule? Thanks in advance! regards, Dr.Shabbirhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Jul 20 13:27:01 2012 From: "sina rastegar sina_rastegar1979/a\yahoo.com" To: CCL Subject: CCL:G: Inquery about Gaussian Jobs Commond Message-Id: <-47255-120720130457-5624-n+xf6Lev23prQXSOGi/Z2A{:}server.ccl.net> X-Original-From: sina rastegar Content-Type: multipart/alternative; boundary="1665047788-856247147-1342803882=:17819" Date: Fri, 20 Jul 2012 10:04:42 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: sina rastegar [sina_rastegar1979]_[yahoo.com] --1665047788-856247147-1342803882=:17819 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi=A0Probably you do not define in your route section the correct basis set= for metalsyou have to use pseudo=3Dread in the route section. please see t= he instruction in gaussian.com about the ecp and basis sets for metals. Regards --- On Fri, 7/20/12, Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com wrote: > From: Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com Subject: CCL:G: Inquery about Gaussian Jobs Commond To: "Rastegar, Sina " Date: Friday, July 20, 2012, 6:42 AM Sent to CCL by: " Bhupesh Kumar Mishra" [bhupesh_chem]*[rediffmail.com] Dear All, I am researcher in field of computational chemistry. I want to optimized Au= and Ag clustes using B3LYP/LANL2DZ basis set using Gaussian09. But it fail= ed indicating an error of internal coordinates systems. I have tried many t= imes with SCF=3DQC or opt(scf=3Dmaxcycles=3D300) but i could not get optimi= zed geometriesand also NBO analysis. It will be very much fruitful if any o= ne suggest me and specific commonds for route section in input file. Your r= esponse is eagerly awaited. With best regards Bhupesh Kr Mishra bhupesh_chem _ rediffmail.com -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0--1665047788-856247147-1342803882=:17819 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi 
Probably you do not define in yo= ur route section the correct basis set for metals
you have to use= pseudo=3Dread in the route section. please see the instruction in gaussian= .com about the ecp and basis sets for metals.

Rega= rds

--- On Fri, 7/20/12, Bhupesh Kumar Mishra bhupesh_chem:_:redi= ffmail.com <owner-chemistry=-=ccl.net> wrote:

From: Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com = <owner-chemistry=-=ccl.net>
Subject: CCL:G: Inquery about Gaussian J= obs Commond
To: "Rastegar, Sina " <sina_rastegar1979=-=yahoo.co= m>
Date: Friday, July 20, 2012, 6:42 AM


Sent to CCL by: " Bhupesh Kumar Mishra" [bhupesh_chem]*[rediffmail.com]
Dear All,
I am researcher in field o= f computational chemistry. I want to optimized Au and Ag clustes using B3LY= P/LANL2DZ basis set using Gaussian09. But it failed indicating an error of = internal coordinates systems. I have tried many times with SCF=3DQC or opt(= scf=3Dmaxcycles=3D300) but i could not get optimized geometriesand also NBO= analysis. It will be very much fruitful if any one suggest me and specific= commonds for route section in input file. Your response is eagerly awaited= .

With best regards
Bhupesh Kr Mishra
bhupesh_chem _ rediffmai= l.com



-=3D This is automatically added to each message by th= e mailing script =3D-
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=
--1665047788-856247147-1342803882=:17819-- From owner-chemistry@ccl.net Fri Jul 20 14:02:01 2012 From: "Jim Kress ccl_nospam^_^kressworks.com" To: CCL Subject: CCL: Visualization software that exports U3D format files Message-Id: <-47256-120720112717-784-fzQf5Qgo0lIrsQJrwHRNnw^server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 Jul 2012 11:27:03 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam!A!kressworks.com] Anyone know of any molecular visualization software that exports 3D molecular visualization data to U3D format? I need to embed 3D, manipulatable objects into PDF files and this is the only path (of which I am aware) to do this. Thanks. Jim Kress From owner-chemistry@ccl.net Fri Jul 20 14:37:00 2012 From: "Andrew Yeung andrew.yeung- -chem.tamu.edu" To: CCL Subject: CCL:G: Inquery about Gaussian Jobs Commond Message-Id: <-47257-120720134134-27153-/COChbspKCb8gIdBYLCb2Q::server.ccl.net> X-Original-From: Andrew Yeung Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 20 Jul 2012 12:41:28 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung]~[chem.tamu.edu] Try opt(cart)? Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 On 2012-07-20 5:42 AM, Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com wrote: > Sent to CCL by: " Bhupesh Kumar Mishra" [bhupesh_chem]*[rediffmail.com] > Dear All, > I am researcher in field of computational chemistry. I want to optimized Au and Ag clustes using B3LYP/LANL2DZ basis set using Gaussian09. But it failed indicating an error of internal coordinates systems. I have tried many times with SCF=QC or opt(scf=maxcycles=300) but i could not get optimized geometriesand also NBO analysis. It will be very much fruitful if any one suggest me and specific commonds for route section in input file. Your response is eagerly awaited. > > With best regards > Bhupesh Kr Mishra > bhupesh_chem _ rediffmail.com> > From owner-chemistry@ccl.net Fri Jul 20 15:12:00 2012 From: "Hao-Bo Guo guohaobo(0)gmail.com" To: CCL Subject: CCL:G: Inquery about Gaussian Jobs Commond Message-Id: <-47258-120720135325-4237-ErhtLqpQ3RUhTY96KsJ1Tg%a%server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/alternative; boundary=bcaec5040a4c31b13504c5469204 Date: Fri, 20 Jul 2012 13:53:17 -0400 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo#%#gmail.com] --bcaec5040a4c31b13504c5469204 Content-Type: text/plain; charset=ISO-8859-1 I think the internal coordinate error often appears for linear system, for which opt=cartesian works. Regards, Hao-Bo Guo On Fri, Jul 20, 2012 at 1:04 PM, sina rastegar sina_rastegar1979/ayahoo.com wrote: > Hi Probably you do not define in your route section the correct basis set > for metalsyou have to use pseudo=read in the route section. please see the > instruction in gaussian.com about the ecp and basis sets for metals. > Regards > > --- On Fri, 7/20/12, Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com ccl.net> wrote: > > > From: Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com ccl.net> > Subject: CCL:G: Inquery about Gaussian Jobs Commond > To: "Rastegar, Sina " > Date: Friday, July 20, 2012, 6:42 AM > > > Sent to CCL by: " Bhupesh Kumar Mishra" [bhupesh_chem]*[rediffmail.com] > Dear All, > I am researcher in field of computational chemistry. I want to optimized > Au and Ag clustes using B3LYP/LANL2DZ basis set using Gaussian09. But it > failed indicating an error of internal coordinates systems. I have tried > many times with SCF=QC or opt(scf=maxcycles=300) but i could not get > optimized geometriesand also NBO analysis. It will be very much fruitful if > any one suggest me and specific commonds for route section in input file. > Your response is eagerly awaited. > > With best regards > Bhupesh Kr Mishra > bhupesh_chem _ rediffmail.com> --1665047788-856247147-1342803882:17819 > Content-Type: text/html; charsetiso-8859-1 > Content-Transfer-Encoding: quoted-printable > >
style="font: inherit;">Hi 
Probably you do not define in your > route section the correct basis set for metals
you have to use > pseudo=read in the route section. please see the instruction in > gaussian.com about the ecp and basis sets for > metals.

Regards

--- On Fri, 7/20/12, > Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com<owner-chemistry:+: > ccl.net> wrote:

From: Bhupesh > Kumar Mishra bhupesh_chem:_:rediffmail.com <owner-chemistry:+:ccl.net>
Subject: > CCL:G: Inquery about Gaussian Jobs Commond
To: "Rastegar, Sina " > <sina_rastegar1979:+:yahoo.com>
Date: Friday, July 20, 2012, > 6:42 AM


Sent to CCL by: " Bhupesh Kumar > Mishra" > [bhupesh_chem]*[rediffmail.com]
Dear All,
I am researcher in field > of computational chemistry. I want to optimized Au and Ag clustes using > B3LYP/LANL2DZ basis set using Gaussian09. But it failed indicating an error > of internal coordinates systems. I have tried many times with SCF=QC or > opt(scf=maxcycles=300) but i could not get optimized geometriesand also NBO > analysis. It will be very much fruitful if any one suggest me and specific > commonds for route section in input file. Your response is eagerly > awaited.

With best regards
Bhupesh Kr Mishra
bhupesh_chem _ > rediffmail.com



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--bcaec5040a4c31b13504c5469204 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I think the internal coordinate error often appears for linear system, for = which opt=3Dcartesian works.

Regards,
Hao-Bo Guo

On Fri, Jul 20, 2012 at 1:04 PM, sina rastegar sina_raste= gar1979/ayahoo.com <= owner-chemistr= y,+,ccl.net> wrote:
Hi=A0Probably you do not define in your rout= e section the correct basis set for metalsyou have to use pseudo=3Dread in = the route section. please see the instruction in gaussian.com about the ecp and basis sets for m= etals.
Regards

--- On Fri, 7/20/12, Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com <owner-chemistry:+:= ccl.net> wrote:

> From: Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com <owner-chemistry:+:ccl.net>
Subject: CCL:G: Inquery about Gaussian Jobs Commond
To: "Rastegar, Sina " <sina_rastegar1979:+:yahoo.com>
Date: Friday, July 20, 2012, 6:42 AM


Sent to CCL by: " Bhupesh Kumar Mishra" [bhupesh_chem]*[rediffmail.com]
Dear All,
I am researcher in field of computational chemistry. I want to optimized Au= and Ag clustes using B3LYP/LANL2DZ basis set using Gaussian09. But it fail= ed indicating an error of internal coordinates systems. I have tried many t= imes with SCF=3DQC or opt(scf=3Dmaxcycles=3D300) but i could not get optimi= zed geometriesand also NBO analysis. It will be very much fruitful if any o= ne suggest me and specific commonds for route section in input file. Your r= esponse is eagerly awaited.

With best regards
Bhupesh Kr Mishra
bhupesh_chem _ rediffma= il.com



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Content-Transfer-Encoding: quoted-printable

<table cellspacing=3D"0" cellpadding=3D"0" border=3D= "0" ><tr><td valign=3D"top" style=3D"f= ont: inherit;">Hi&nbsp;<div>Probably you do not define in= your route section the correct basis set for metals</div><div>= you have to use pseudo=3Dread in the route section. please see the instruct= ion in gaussian.com a= bout the ecp and basis sets for metals.</div><div><br><= ;/div><div>Regards<br><br>--- On <b>Fri, 7/20/12= , Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com <i>&lt;owner-chemistry:+:ccl.net&gt;</i></b&= gt; wrote:<br><blockquote style=3D"border-left: 2px solid rgb= (16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From= : Bhupesh Kumar Mishra bhupesh_chem:_:rediffmail.com &lt;owner-chemistry:+:ccl.net&gt;<br>Subject: CCL:G: = Inquery about Gaussian Jobs Commond<br>To: "Rastegar, Sina "= ; &lt;sina_rastegar1979:+:yahoo.com&gt;<br>Date: Friday, July 20, 2012, 6:42 AM<br= ><br><div class=3D"plainMail"><br>Sent to CC= L by: " Bhupesh Kumar Mishra"
=A0[bhupesh_chem]*[redi= ffmail.com]<br>Dear All,<br>I am researcher in field of com= putational chemistry. I want to optimized Au and Ag clustes using B3LYP/LAN= L2DZ basis set using Gaussian09. But it failed indicating an error of inter= nal coordinates systems. I have tried many times with SCF=3DQC or opt(scf= =3Dmaxcycles=3D300) but i could not get optimized geometriesand also NBO an= alysis. It will be very much fruitful if any one suggest me and specific co= mmonds for route section in input file. Your response is eagerly awaited.&l= t;br><br>With best regards<br>Bhupesh Kr Mishra<br>bhu= pesh_chem _ rediffmail.= com<br><br><br><br>-=3D This is automatically a= dded to each message by the mailing script =3D-<br>To recover the ema= il address of the author of the message, please change<br>the strange= characters on the top line to the :+: sign. You can also<br<br>&l= t;br>E-mail to subscribers: <a ymailto=3D"mailto:CHEMISTRY:+:= ccl.net"
=A0href=3D"/mc/compose?to=3DCHEMISTRY:+:ccl.net">CHEMISTRY:+:ccl.net</a> or use:<br>&nbsp; &nb= sp; &nbsp; <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_cc= l_message" target=3D"_blank">http://www.ccl.net/cg= i-bin/ccl/send_ccl_message</a><br><br>E-mail to admin= istrators: <a ymailto=3D"mailto:CHEMISTRY-REQUEST:+:ccl.= net" href=3D"/mc/compose?to=3DCHEMISTRY-REQUEST:+:ccl.net">CHEMISTRY-REQUEST:+:= ccl.net</a> or use&l= t;br>&nbsp; &nbsp; &nbsp; <a href=3D"http://www.c= cl.net/cgi-bin/ccl/send_ccl_message" target=3D"_blank"&g= t;http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>= ;<br<br>&nbsp; &nbsp; &nbsp; <a href=3D"http:/= /www.ccl.net/chemistry/sub_unsub.shtml" target=3D"_blank"= ;>http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>&l= t;br>Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=3D= "_blank">http= ://www.ccl.net</a><br><br>Job: <a href=3D"http://www.ccl.net/jobs<= /a>" target=3D"_blank">http://www.ccl.net/jobs</a> <br>Confere= nces: <a
=A0href=3D"http://server.ccl.net/chemistry/announcements= /conferences/" target=3D"_blank">http:/= /server.ccl.net/chemistry/announcements/conferences/</a><br>= ;<br>Search Messages: <a href=3D"http://www.ccl.net/che= mistry/searchccl/index.shtml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</a><br>= <br<br>&nbsp; &nbsp; &nbsp; <a href=3D"http://www.ccl.net/s= pammers.txt" target=3D"_blank">http://www.ccl.net/spammers.txt= </a><br><br>RTFI: <a href=3D"http://www.cc= l.net/chemistry/aboutccl/instructions/" target=3D"_blank"= ;>http://www.ccl.net/chemistry/aboutccl/instructions/</a&g= t;<br><br><br></div></blockquote></div>= </td></tr></table>

--bcaec5040a4c31b13504c5469204-- From owner-chemistry@ccl.net Fri Jul 20 23:47:00 2012 From: "Jan Labanowski janl-.-speakeasy.net" To: CCL Subject: CCL: CCL may die unexpectedly... Message-Id: <-47259-120720234614-11774-3RpsV2yi+fftzOctASjPbg(_)server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Fri, 20 Jul 2012 23:46:00 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl++speakeasy.net] Dear CCL Faithful, I am taking a week off and I will try to stay away from Internet as much as I can (I can't really, but I will try to impose it "envirnmentally" by eating wild blueberries rather than tapping on the keyboard). So, things will be slow, especially with the messages that are stopped for my review. However, if power goes off or some malicious piece of crud messes up my computers, I will not be around to "push the button" and you will get some rest from messages whose subject starts from CCL:. So, in short, expect the unexpected and take it easy. Luckily, nobody's life depends on CCL. Evan I do not believe in this... Jan -- Jan Labanowski CCL Maintainer