From owner-chemistry@ccl.net Wed May 4 00:18:01 2011 From: "Jon Cody Haines jch..molysym.com" To: CCL Subject: CCL: Ball & Stick: Molecular Visualization App for the iPad now available. Message-Id: <-44525-110503205634-17375-j9VzQDQ0EKdLnWp51kBV4w:-:server.ccl.net> X-Original-From: "Jon Cody Haines" Date: Tue, 3 May 2011 20:56:32 -0400 Sent to CCL by: "Jon Cody Haines" [jch ~~ molysym.com] Ball & Stick: A new high-quality molecular visualization app for the iPad is now available. Find out more here: http://itunes.apple.com/us/app/ball-stick/id434305371?mt=8 MolySym develops hardware and software science educational tools with a focus on chemistry. Find out more here: http://www.molysym.com/ From owner-chemistry@ccl.net Wed May 4 00:53:00 2011 From: "Igor Filippov igor.v.filippov#gmail.com" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44526-110503190644-2643-kuKb8zVL7wTJa5dpjg0yDw]-[server.ccl.net> X-Original-From: Igor Filippov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Tue, 03 May 2011 19:06:28 -0400 Mime-Version: 1.0 Sent to CCL by: Igor Filippov [igor.v.filippov!A!gmail.com] I know I shouldn't feed the trolls but this is getting ridiculous. Where is this "evil" you're speaking of? If you want to learn about evil, read this http://www.gnu.org/philosophy/right-to-read.html Best, Igor On Tue, 2011-05-03 at 12:53 -0400, Jim Kress ccl_nospam++kressworks.com wrote: > Nice try but unresponsive. You can rationalize evil all you want, but > it is still evil. > > > > Jim Kress > > > > From: owner-chemistry+ccl_nospam==kressworks.com[-]ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com[-]ccl.net] On > Behalf Of David A Mannock dmannock,ualberta.ca > Sent: Monday, May 02, 2011 5:29 PM > To: Kress, Jim > Subject: CCL: To begin with computational chemistry > > > > > Jim, I know. I feel guilty every time a take an egg from a chicken or > go to a cut-price movie theatre. lol The unfortunate reality is that > in the third world piracy of software and text books is commonplace > and there is little that we can do to stop it. In order to stop it and > bring those countries into line, there have to be electronic options > put in place for teaching purposes. Once qualified, many of those > people will probably buy a hard copy to put on their bookshelf if they > continue in science. Personally, I smile when I see someone copy a > paragraph or two from one of my papers into their own "original" work. > In reality, since knowledge is power, and I occasionally have to pay > an advertizing fee to publish, I wonder if I should not be getting a > royalty payment everytime someone downloads or photocopies my papers. > Hmm! I wonder if I could afford a Lamborghini just like my brothers > after all? Dave > > On Mon, May 2, 2011 at 11:48 AM, Jim Kress ccl_nospam++kressworks.com > wrote: > > There is no justification for theft. > > > > Jim Kress > > > > > From: owner-chemistry+ccl_nospam==kressworks.com]_[ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com]_[ccl.net] On > Behalf Of > David A Mannock dmannock(-)ualberta.ca > Sent: Saturday, April 30, 2011 5:13 PM > To: Kress, Jim > Subject: CCL: To begin with computational chemistry > > > > Chris, as a newbie to computational chemistry, I try to use every > resource > that I can get hold of. I have to admit that I sometimes pirate > electronic > copies to help me search texts which are often long and complicated. A > recent point relevant to this issue is Jacob Israelachvili's > "Intermolecular > and surface forces", 2nd Edn. As our lab copy disappeared into a black > hole > known as my colleagues basement, I found a pirated online copy of this > essential text. I later bought a second-hand hard copy, while awaiting > the > appearance of the 3rd Edition, which was due to appear in 2010, but > came out > in 2011. I have read the 1991 2nd edition cover to cover and have > returned > to it in order to refresh my memory many times. After talking to Jacob > Israelachvili, he explained the delays in getting the 3rd edition to > press > and told me when it would be available. Within a week of it coming off > the > presses, I had bought a copy from Amazon out of my own pocket. The new > edition is several hundred pages longer than the previous copy and an > electronic version would be useful to me. It is a beautifully written > masterpiece in my opinion. However, many publishers are slow in their > move > into the electronic realm. This is where the future lies. > > My job ends here on June 30th, 2011, but I still have responsibilities > for > writing up papers for a student. I will not have access to online > library > facilities here because of local University policy. Despite this, I > would > still be willing to buy a new edition of your book to help with my > calculations on my Linux box. I would do this out of my own pocket if > need > be. > > As I see it, one of the main purposes of text books is to put all of > the > knowledge in a certain area in one place for ease of reference. I > think that > this is very valuable for those of us who do research and those who > teach. > Putting together a new edition of your book would be recognized as a > valuable contribution by people in this scientific area, but rather > than be > pessimistic about piracy, ask your publishers to make an electronic > copy > available for sale at 50% of the price of the softcover. A university > could > either buy a yearly site license for distribution to students at a > lower > price, or the institution could host a copy which could be read > online, but > not downloaded. There will always be people who want to get something > for > nothing and who are willing to remove the encryption on electronic > media, > the simplest solution is to make the text available at a lower cost > for > academic use and make some money rather than none. You should be > talking to > your publisher about this policy, as it will help their bottom line > and your > standard of living in your retirement!! So cheer up and realize that > old > dogs, like myself, would rather sit on a sun lounger on my back porch > reading your new edition, than sitting at a computer screen in the lab > or in > my study! David Mannock > > On Sat, Apr 30, 2011 at 12:46 PM, Christopher Cramer cramer+/-umn.edu > wrote: > > > Sent to CCL by: Christopher Cramer [cramer-$-umn.edu] > My... > > The least you can do if you're going to steal the book, and post it > online > for piracy, is choose a later printing -- then people won't have to > refer to > so many errata. > > Now I recall why I've been reluctant to devote the time to a 3rd > edition... > > CJC > > On Apr 30, 2011, at 12:30 PM, Deepangi Pandit > deepangi.pandita/gmail.com > wrote: > > > > > Sent to CCL by: Deepangi Pandit [deepangi.pandit_-_gmail.com] > > Hi Bhargav: > > You can refer "Essentials of Computational Chemistry: Theories and > > Models" by Christopher J. Cramer > > > > > http://kimia.unnes.ac.id/kasmui/textbooks/Essentials%20of% > 20Computational%20 > Chemistry%20Theories%20and%20Models%202d%20Ed%20-%20Christopher%20J.% > 20Crame > r.pdf > > > > ShortURL > > > > http://alturl.com/jks5j > > > > Also please feel free to browse > > > > > http://static.msi.umn.edu/tutorial/chemistryphysics/IntroCompChem.pdf > > > > I believe these are good starting points and based on your interests > > you can explore the topic/s further. > > > > Regards, > > Deepa > > > > > > > > On Sat, Apr 30, 2011 at 6:20 AM, Bhargav Trivedi > > bhargavatrivedi*|*gmail.com wrote: > >> > >> Sent to CCL by: "Bhargav Trivedi" [bhargavatrivedi[-]gmail.com] > >> Dear all, > >> I would like to learn computational chemistry. Please tell me how > can I > prepare for it. > >> I am an M Sc PhD with Physical chemistry & an academician since > last 16 > years. I teach thermodynamics and electrochemistry to under graduates. > >> Thanks a lot: > >> Dr. Bhargav Trivedi, > >> Associate Professor of Chemistry, > >> J & J College of science, > >> Nadiad, Gujarat. > >> India> > > > > -- > > Christopher J. Cramer > Elmore H. Northey Professor > University of Minnesota > Department of Chemistry > 207 Pleasant St. SE > Minneapolis, MN 55455-0431 > -------------------------- > Phone: (612) 624-0859 || FAX: (612) > 626-7541 > > Mobile: (952) 297-2575 > email: cramer,+,umn.edu > jabber: cramer,+,jabber.umn.edu > http://pollux.chem.umn.edu/~cramer 7Ecramer> > (website includes information about the textbook "Essentials > of Computational Chemistry: Theories and Models, 2nd Edition")
> > E-mail to subscribers: CHEMISTRY++ccl.net or use:E-mail to > administrators: CHEMISTRY-REQUEST++ccl.net or > usehttp://www.ccl.net/chemistry/sub_unsub.shtml Content-Type: text/html; > charset="us-ascii" > Content-Transfer-Encoding: quoted-printable > > xmlns:o=3D"urn:schemas-microsoft-com:office:office" = > xmlns:w=3D"urn:schemas-microsoft-com:office:word" = > xmlns:m=3D"http://schemas.microsoft.com/office/2004/12/omml" = > xmlns=3D"http://www.w3.org/TR/REC-html40"> http-equiv=3DContent-Type content=3D"text/html; = > charset=3Dus-ascii"> 12 = > (filtered medium)"> link=3Dblue = > vlink=3Dpurple>

style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497= > D'>There is no justification for theft.

class=3DMsoNormal> style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497= > D'> 

style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497= > D'>Jim Kress

style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497= > D'> 

style=3D'border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in > = > 4.0pt'>
1.0pt;padding:3.0pt 0in 0in 0in'>

style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:= > style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'> = > owner-chemistry+ccl_nospam=3D=3Dkressworks.com]_[ccl.net = > [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com]_[ccl.net] > On = > Behalf Of David A Mannock dmannock(-)ualberta.ca
Sent: = > Saturday, April 30, 2011 5:13 PM
To: Kress, Jim = >
Subject: CCL: To begin with computational = > chemistry

class=3DMsoNormal> 

style=3D'margin-bottom:12.0pt'>Chris, as a newbie to computational = > chemistry, I try to use every resource that I can get hold of. I have > to = > admit that I sometimes pirate electronic copies to help me search > texts = > which are often long and complicated. A recent point relevant to this > = > issue is Jacob Israelachvili's "Intermolecular and surface = > forces", 2nd Edn. As our lab copy disappeared into a black hole = > known as my colleagues basement, I found a pirated online copy of this > = > essential text. I later bought a second-hand hard copy, while awaiting > = > the appearance of the 3rd Edition, which was due to appear in 2010, > but = > came out in 2011. I have read the 1991 2nd edition cover to cover and > = > have returned to it in order to refresh my memory many times. After = > talking to Jacob Israelachvili, he explained the delays in getting the > = > 3rd edition to press and told me when it would be available. Within a > = > week of it coming off the presses, I had bought a copy from Amazon out > = > of my own pocket. The new edition is several hundred pages longer than > = > the previous copy and an electronic version would be useful to me. It > is = > a beautifully written masterpiece in my opinion. However, many = > publishers are slow in their move into the electronic realm. This is = > where the future lies.

My job ends here on June 30th, 2011, but > I = > still have responsibilities for writing up papers for a student. I > will = > not have access to online library facilities here because of local = > University policy. Despite this, I would still be willing to buy a new > = > edition of your book to help with my calculations on my Linux box. I = > would do this out of my own pocket if need be.

As I see it, > one = > of the main purposes of text books is to put all of the knowledge in a > = > certain area in one place for ease of reference. I think that this is > = > very valuable for those of us who do research and those who teach. = > Putting together a new edition of your book would be recognized as a = > valuable contribution by people in this scientific area, but rather > than = > be pessimistic about piracy, ask your publishers to make an electronic > = > copy available for sale at 50% of the price of the softcover. A = > university could either buy a yearly site license for distribution to > = > students at a lower price, or the institution could host a copy which > = > could be read online, but not downloaded. There will always be people > = > who want to get something for nothing and who are willing to remove > the = > encryption on electronic media, the simplest solution is to make the = > text available at a lower cost for academic use and make some money = > rather than none. You should be talking to your publisher about this = > policy, as it will help their bottom line and your standard of living > in = > your retirement!! So cheer up and realize that old dogs, like myself, > = > would rather sit on a sun lounger on my back porch reading your new = > edition, than sitting at a computer screen in the lab or in my study! > = > David Mannock 

On Sat, > Apr = > 30, 2011 at 12:46 PM, Christopher Cramer cramer+/- href=3D"http://umn.edu">umn.edu < href=3D"mailto:owner-chemistry++ccl.net">owner-chemistry > ++ccl.net>= > wrote:

style=3D'margin-bottom:12.0pt'>
Sent to CCL by: Christopher Cramer > = > [cramer-$- target=3D"_blank">umn.edu]
My...

The least you can do if > = > you're going to steal the book, and post it online for piracy, is > choose = > a later printing -- then people won't have to refer to so many = > errata.

Now I recall why I've been reluctant to devote the time > = > to a 3rd edition...

CJC

On Apr 30, 2011, at 12:30 PM, = > Deepangi Pandit deepangi.pandita/ target=3D"_blank">gmail.com wrote:

>
> Sent to CCL > = > by: Deepangi Pandit [ target=3D"_blank">deepangi.pandit_-_gmail.com]
> Hi = > Bhargav:
> You can refer "Essentials of Computational = > Chemistry: Theories and
> Models" by Christopher J. = > Cramer
>
> href=3D"http://kimia.unnes.ac.id/kasmui/textbooks/Essentials%20of% > 20Compu= > tational%20Chemistry%20Theories%20and%20Models%202d%20Ed%20-% > 20Christophe= > r%20J.%20Cramer.pdf" = > target=3D"_blank">http://kimia.unnes.ac.id/kasmui/textbooks/Essentials > %20= > of%20Computational%20Chemistry%20Theories%20and%20Models%202d%20Ed% > 20-%20= > Christopher%20J.%20Cramer.pdf
>
> = > ShortURL
>
> target=3D"_blank">http://alturl.com/jks5j
>
> Also = > please feel free to browse
>
> href=3D"http://static.msi.umn.edu/tutorial/chemistryphysics/IntroCompChem= > .pdf" = > target=3D"_blank">http://static.msi.umn.edu/tutorial/chemistryphysics/Int= > roCompChem.pdf
>
> I believe these are good starting = > points and based on your interests
> you can explore the topic/s > = > further.
>
> Regards,
> = > Deepa
>
>
>
> On Sat, Apr 30, 2011 at 6:20 AM, > = > Bhargav Trivedi
> bhargavatrivedi*|* = > target=3D"_blank">gmail.com <owner-chemistry~!~ href=3D"http://ccl.net" target=3D"_blank">ccl.net> = > wrote:
>>
>> Sent to CCL by: "Bhargav = >  Trivedi" [bhargavatrivedi[-] target=3D"_blank">gmail.com]
>> Dear all,
>> I = > would like to learn computational chemistry. Please tell me how can I > = > prepare for it.
>> I am an M Sc PhD with Physical chemistry = > & an academician since last 16 years. I teach thermodynamics and = > electrochemistry to under graduates.
>> Thanks a = > lot:
>> Dr. Bhargav Trivedi,
>> Associate Professor > of = > Chemistry,
>> J & J College of science,
>> > Nadiad, = > Gujarat.
>> India>
>

--

Christopher J. > = > Cramer
Elmore H. Northey Professor
University of = > Minnesota
Department of Chemistry
207 Pleasant St. = > SE
Minneapolis, MN > 55455-0431
--------------------------
Phone: = >  (612) 624-0859 || FAX: > = >  (612) > 626-7541
Mobile: = > (952) 297-2575
email: = >  cramer,+, target=3D"_blank">umn.edu
jabber:  cramer,+, href=3D"http://jabber.umn.edu" = > target=3D"_blank">jabber.umn.edu
href=3D"http://pollux.chem.umn.edu/%7Ecramer" = > target=3D"_blank">http://pollux.chem.umn.edu/~cramer
(website = > includes information about the textbook "Essentials
  = >  of Computational Chemistry:  Theories and Models, 2nd = > Edition")



-=3D This is automatically added to each > = > message by the mailing script =3D-<br


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> > > > > From owner-chemistry@ccl.net Wed May 4 01:28:00 2011 From: "Joseph Corkery jcorkery%%eyesopen.com" To: CCL Subject: CCL: OpenEye seminar in Shanghai - May 16th Message-Id: <-44527-110503220344-18693-aNtca1aanmyfriURJUlwgA*_*server.ccl.net> X-Original-From: Joseph Corkery Content-Type: multipart/alternative; boundary="Apple-Mail-53--250100199" Date: Tue, 3 May 2011 22:03:34 -0400 MIME-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Joseph Corkery [jcorkery~!~eyesopen.com] --Apple-Mail-53--250100199 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="windows-1252" Dear CCL subscribers, You are invited to attend a one day seminar hosted by OpenEye Scientific = Software in Shanghai on Monday, May 16th at the Parkyard Hotel Shanghai. = There is no fee to attend the seminar, but space is limited, so please = register by emailing china~~eyesopen.com soon. The agenda and speaker biographies follow. For additional details = regarding the seminar please visit the following website: http://www.eyesopen.com/events/shanghai-conference AGENDA 09:30 Welcome 09:45 Plenary: Modeling impact in drug discovery: Selected highlights = of 18 years in discovery research =96 Christopher Bayly 10:15 Solving some current problems in docking - Increasing = reliability in structure-based virtual screening and pose prediction = with ligand information =96 Paul Hawkins 11:15 Coffee break 11:30 SZYBKI: Removing the guesswork from ligand entropy =96 = Christopher Bayly 12:00 Buffet Lunch 13:15 Ligand-based virtual screening =96 using shape and = electrostatics for rapid and efficient detection of bioactive molecules = =96 Paul Hawkins 14:15 Fragment-based methods in lead optimization =96 applying shape = and electrostatics to multi-objective property optimization, bioisostere = identification & lead hopping =96 Paul Hawkins 14:45 Coffee break 15:00 SZMAP: Changing structured water from a liability into an = advantage =96 Christopher Bayly 15:45 Conclusion 16:00 Reception SPEAKERS: Christopher Bayly, Ph.D. - Senior Scientist, OpenEye Scientific Software Starting off with a B.Sc. in Honours Biochemistry from Bishop=92s = University, Christopher went on to attain a Master=92s in bio-organic = chemistry with Pierre Deslongchamps at L=92Universite de Sherbrooke. = Still driven by an enduring interest in harnessing the physical = chemistry of biological systems, he switched to theoretical chemistry, = going on to do his Ph.D. with Friedrich Grein at the University of New = Brunswick. This was followed by a stimulating postdoctoral term in Peter = Kollman's Theoretical Biophysical Chemistry group at UCSF, where he = focused on critical force-field methods for biomolecular simulations = (the RESP method for the AMBER forcefield). In 1992 he joined the Merck = Frosst Centre for Therapeutic Research in Montreal to introduce = computational chemistry methods into their pharmaceutical discovery = programs. Over the 18 years he was with Merck Frosst, he founded and = built up the Chemistry Modeling and Informatics group there, leading it = right through to the closure of the research site in 2010. While working = in drug discovery he continued external collaborations and the = development of new methods (including ligand charging with AM1-BCC and = molecular polarization using EPIC). Starting in 2011, he took up a = position as Senior Scientist with OpenEye Scientific Software, where he = is continuing his pursuit of developing computational chemistry novel = methods to help drug discovery. Paul Hawkins, Ph.D. - Senior Applications Scientist, OpenEye Scientific = Software Paul Hawkins did his Ph.D. at "the home of golf", St. Andrews and was a = NATO post-doctoral fellow at Pennsylvania State before settling in = Boston to work in biotech as a medicinal chemist. In this capacity he = was involved in a variety of project areas, including kinase inhibition = and anti-bacterial agents. After a number of years at thebench he moved = > from practical to computational chemistry and became an applications = scientist for Tripos, working with SYBYL. In 2005 he became OpenEye's = first applications scientist, and since then has focused on problems in = conformer generation and the application of shape and electrostatic = similarity methods to drug discovery. --Apple-Mail-53--250100199 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="windows-1252" You are invited to attend a one day seminar hosted by = OpenEye Scientific Software in Shanghai on Monday, May 16th at the = Parkyard Hotel Shanghai. There is no fee to attend the seminar, but = space is limited, so please register by emailing china~~eyesopen.com = soon.
The agenda and speaker biographies follow. = For additional details regarding the seminar please visit the following = website:


= --Apple-Mail-53--250100199-- From owner-chemistry@ccl.net Wed May 4 02:03:00 2011 From: "Mihaly Mezei Mihaly.Mezei*o*mssm.edu" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44528-110504003312-14851-vBkHyys8R/RKLRyl6wR2Fg:_:server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Wed, 04 May 2011 00:33:02 -0400 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei-#-mssm.edu] ----- Original Message ----- > From: "Jim Kress ccl_nospam++kressworks.com" Date: Tuesday, May 3, 2011 12:53 pm Subject: CCL: To begin with computational chemistry > Nice try but unresponsive. You can rationalize evil all you want, but it is still evil. Let's keep things in perspective. If violating copyright is evil, what do you call mass murder? Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Wed May 4 02:38:01 2011 From: "Deepthi Jose deepthi,iisertvm.ac.in" To: CCL Subject: CCL:G: MO6 Message-Id: <-44529-110504003336-15310-TxsjKqnMnuDgw0xZrFtrpA=server.ccl.net> X-Original-From: Deepthi Jose Content-Type: multipart/alternative; boundary=20cf30549b1104795104a26bc2c5 Date: Wed, 4 May 2011 10:03:27 +0530 MIME-Version: 1.0 Sent to CCL by: Deepthi Jose [deepthi=-=iisertvm.ac.in] --20cf30549b1104795104a26bc2c5 Content-Type: text/plain; charset=ISO-8859-1 Dear Sujit, The functional is M06 (MZeroSix) not MO6. Regards Deepthi On Wed, May 4, 2011 at 5:05 AM, Sujit Kumar Mondal sujitharvard###gmail.com wrote: > *Hi all* > *I am sujit, i am working with Gaussian-09 very recently(2months)/ can be > described as a beginnner. I am very much using B3lyp hybrid-function for > verious calculation such geometry opt, IRC, Scrf etc but recently i am > facing problem with MO6 function for IRC calculation!! * > *1)# MO6/6-311+G(d,p) IRC=(calcfc,maxcycle=1000) > scf=(tight,maxcycle=1000,cdiis) showing me all the time* *syntax error!! can > anyone tell me what kind of mistake I am making during my input command in > the route section?* > ** > *2)# MO6/6-311+G(d,p) opt scf=(tight, cdiis) for Fe+3 complex, link died > couple of times after 30min of run!! I do not know the reason behind it, > though b3lyp gave nice results, anybody can suggest what will be the > probable problem for this case?* > > *3)# MO6/6-311+G(d,p) opt=(calcall,maxcycle=600) > scf=(tight,maxcycle=600,cdiis) Also I am having problem for frequency > calculation using MO6, syntax error, please correct my mistake?* > ** > *Looking forward for suggestions* > ** > *Sujit* > ** > ** > --20cf30549b1104795104a26bc2c5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sujit,
The functional is M06 (MZeroSix) not MO6.



Reg= ards
Deepthi

On Wed, May 4, 2011 at 5:= 05 AM, Sujit Kumar Mondal sujitharvard###gmail= .com <o= wner-chemistry/a\ccl.net> wrote:
Hi all
I am sujit, i am working with=A0Gaussian-09 very recently(2months)/= can be described as a beginnner. I am very much using B3lyp hybrid-functio= n for verious calculation such geometry opt, IRC, Scrf etc but recently i a= m facing problem with MO6 function for IRC calculation!!
1)# MO6/6-311+G(d,p) IRC=3D(calcfc,maxcycle=3D1000) scf=3D(tight,ma= xcycle=3D1000,cdiis) showing me all the time syntax error!!=A0can anyone tell me what ki= nd of mistake I am=A0making during my input command in the route section?
=A0
2)# MO6/6-311+G(d,p) opt scf=3D(tight, cdiis) for Fe+3 complex,=A0l= ink died couple of times after 30min of run!! I do not know the reason behi= nd it, though b3lyp gave nice results, =A0anybody can suggest what will be = the probable=A0problem for this case?
=A0
3)# MO6/6-311+G(d,p) opt=3D(calcall,maxcycle=3D600) scf=3D(tight,ma= xcycle=3D600,cdiis)=A0Also=A0I am having problem for frequency calculation = using MO6, syntax error, please correct my mistake?=
=A0
Looking forward for suggestions<= /div>
=A0
Sujit
=A0
=A0

--20cf30549b1104795104a26bc2c5-- From owner-chemistry@ccl.net Wed May 4 03:13:00 2011 From: "aloysius bella aloysius.bella:+:gmail.com" To: CCL Subject: CCL: CCL-G-MO6 Message-Id: <-44530-110504012532-26931-/AnAKzdO8VHpqf0Ptd8jIw|server.ccl.net> X-Original-From: aloysius bella Content-Type: multipart/alternative; boundary=001485f92bdcc9f1b604a26c7b82 Date: Wed, 4 May 2011 10:55:23 +0530 MIME-Version: 1.0 Sent to CCL by: aloysius bella [aloysius.bella,gmail.com] --001485f92bdcc9f1b604a26c7b82 Content-Type: text/plain; charset=ISO-8859-1 Hi Sujit, Do check whether you have typed MO6 or M06. You should put M(zero i.e.,number)6 ,  not M(O-alphabet)6. try. regards, Bella. -- Regards, A. Bella, --001485f92bdcc9f1b604a26c7b82 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 
Hi=
 Sujit,
Do check whether you have typed MO6 or M06. You should put M(zer=
o i.e.,number)6 ,&nbsp; not M(O-alphabet)6. try.
regards,
Bella.<=
/font>


--
=A0=A0=A0
Regards,
A. Bella,

<= br> --001485f92bdcc9f1b604a26c7b82-- From owner-chemistry@ccl.net Wed May 4 03:48:00 2011 From: "Jacopo Sgrignani sgrigna{:}gmail.com" To: CCL Subject: CCL: RNA plot Message-Id: <-44531-110503090707-18795-RwfKvVQGXEpiuB5zSlYXlw() server.ccl.net> X-Original-From: Jacopo Sgrignani Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 3 May 2011 15:06:58 +0200 MIME-Version: 1.0 Sent to CCL by: Jacopo Sgrignani [sgrigna.|a|.gmail.com] Dear all could anybody suggest me a software to make a plot similar to the figure 1A of this paper ? http://www.sciencemag.org/content/326/5957/1271/F1.large.jpg Thanks a lot Jacopo From owner-chemistry@ccl.net Wed May 4 04:22:00 2011 From: "Johannes Johansson johjo76^^gmail.com" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44532-110504030653-29703-1olXXgSnJ5EOhBnTTITEyg~!~server.ccl.net> X-Original-From: Johannes Johansson Content-Type: text/plain; charset=UTF-8 Date: Wed, 4 May 2011 09:06:42 +0200 MIME-Version: 1.0 Sent to CCL by: Johannes Johansson [johjo76:+:gmail.com] No offence, but please stop using "Good" and "Evil", these are religious concepts, nothing to do with reality. This is a scientific forum! 2011/5/4, Mihaly Mezei Mihaly.Mezei*o*mssm.edu : > > Sent to CCL by: Mihaly Mezei [Mihaly.Mezei-#-mssm.edu] > > > > > ----- Original Message ----- >> From: "Jim Kress ccl_nospam++kressworks.com" > Date: Tuesday, May 3, 2011 12:53 pm > Subject: CCL: To begin with computational chemistry > >> Nice try but unresponsive. You can rationalize evil all you want, but it >> is still evil. > Let's keep things in perspective. If violating copyright is evil, what do > you call mass murder? > > Mihaly Mezei > > Department of Structural and Chemical Biology, Mount Sinai School of > Medicine > Voice: (212) 659-5475 Fax: (212) 849-2456 > WWW (MSSM home): > http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > WWW (Department): http://atlas.physbio.mssm.edu> > > -- Adam Johannes Johansson Ph.D., M.Sc. Division of Physical Chemistry KTH (Royal Institute of Technology) Teknikringen 36 SE-100 44 Stockholm Sweden Office: 087908217 Cell phone: 0708178487 E-mail:johjo76]=[gmail.com Research web page:www.physto.se/~johjo From owner-chemistry@ccl.net Wed May 4 08:15:01 2011 From: "Aloysius Bella aloysius.bella[-]rediffmail.com" To: CCL Subject: CCL:G: =?utf-8?B?UmU6IENDTDpHOiBNTzY=?= Message-Id: <-44533-110504011013-8809-ff+hO6x7t1ci9eNNFkVyZw^-^server.ccl.net> X-Original-From: "Aloysius Bella" Content-Type: multipart/alternative; boundary="=_fb2bce7ba9d2cfd26fb5ac1f46fd39b7" Date: 4 May 2011 05:09:14 -0000 MIME-Version: 1.0 Sent to CCL by: "Aloysius Bella" [aloysius.bella#,#rediffmail.com] --=_fb2bce7ba9d2cfd26fb5ac1f46fd39b7 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Hi Sujit, Do check whether you have typed MO6 or M06. You should put M(zero i.e.,number)6 ,  not M(O-alphabet)6. try. regards, Bella. On Wed, 04 May 2011 09:35:04 +0530 "Sujit Kumar Mondal sujitharvard###gmail.com" <owner-chemistry .. ccl.net> wrote >Hi allI am sujit, i am working with Gaussian-09 very recently(2months)/ can be described as a beginnner. I am very much using B3lyp hybrid-function for verious calculation such geometry opt, IRC, Scrf etc but recently i am facing problem with MO6 function for IRC calculation!! 1)# MO6/6-311+G(d,p) IRC=(calcfc,maxcycle=1000) scf=(tight,maxcycle=1000,cdiis) showing me all the time syntax error!! can anyone tell me what kind of mistake I am making during my input command in the route section? 2)# MO6/6-311+G(d,p) opt scf=(tight, cdiis) for Fe+3 complex, link died couple of times after 30min of run!! I do not know the reason behind it, though b3lyp gave nice results,  anybody can suggest what will be the probable problem for this case? 3)# MO6/6-311+G(d,p) opt=(calcall,maxcycle=600) scf=(tight,maxcycle=600,cdiis) Also I am having problem for frequency calculation using MO6, syntax error, please correct my mistake? Looking forward for suggestions Sujit   --=_fb2bce7ba9d2cfd26fb5ac1f46fd39b7 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="UTF-8" Hi Sujit,
Do check whether you have typed MO6 or M06. You should put M(z= ero i.e.,number)6 ,  not M(O-alphabet)6. try.
regards,
Bella. On Wed, 04 May 2011 09:35:04 +0530 "Sujit Kumar Mondal sujitharvard###gmail= .com" <owner-chemistry .. ccl.net> wrote
>
Hi all
I am sujit, i am working= with Gaussian-09 very recently(2months)/ can be described as a beginn= ner. I am very much using B3lyp hybrid-function for verious calculation suc= h geometry opt, IRC, Scrf etc but recently i am facing problem with MO6 fun= ction for IRC calculation!!
1)# MO6/6-311+G(d,p= ) IRC=3D(calcfc,maxcycle=3D1000) scf=3D(tight,maxcycle=3D1000,cdiis) showin= g me all the time syntax error!!&n= bsp;can anyone tell me what kind of mistake = I am making during my input command in the route section?
 
2)# MO6/6-311+G(d,p= ) opt scf=3D(tight, cdiis) for Fe+3 complex, link died couple of times= after 30min of run!! I do not know the reason behind it, though b3lyp gave= nice results,  anybody can suggest what will be the probable pro= blem for this case?
 
3)# MO6/6-3= 11+G(d,p) opt=3D(calcall,maxcycle=3D600) scf=3D(tight,maxcycle=3D600,cdiis)=  Also I am having problem for frequency calculation using MO6, syntax error, please correct my mistake?
 
<= div>Looking forward for suggestions<= /strong>
 
Sujit
 
 

--=_fb2bce7ba9d2cfd26fb5ac1f46fd39b7-- From owner-chemistry@ccl.net Wed May 4 08:50:00 2011 From: "Sascha Hausberg sascha.hausberg|*|aci.uni-heidelberg.de" To: CCL Subject: CCL: Modeling of Molecular Properties, Heidelberg, October 9-11 Message-Id: <-44534-110504070407-27623-DPZiv7JIofsr63Ied2eyNQ###server.ccl.net> X-Original-From: "Sascha Hausberg" Date: Wed, 4 May 2011 07:04:05 -0400 Sent to CCL by: "Sascha Hausberg" [sascha.hausberg,+,aci.uni-heidelberg.de] Dear colleagues, we cordially invite you to the final meeting of the Graduate College 850 'Modeling of Molecular Properties' at Heidelberg University on October 9-11, 2011. Our program includes lectures by Gernot Frenking, Stefan Grimme, Frank Neese, Markus Reiher, Peter Schwerdtfeger, Sason Shaik and other outstanding speakers. Further information and the complete list of speakers can be found via http://molmod2011.uni-hd.de Registration is open and early registration will be available until May 31st. The modest registration fee covers the welcome reception and conference dinner. An early registration is recommended since we expect a large number of delegates, the number of attendees and scientific contributions, however, is limited. We hope in particular to attract many PhD students and postdoctoral fellows. We would be very pleased to welcome you in Heidelberg later this year. Best regards The Organization Committee, Peter Comba molmod2011-$-aci.uni-heidelberg.de From owner-chemistry@ccl.net Wed May 4 09:25:00 2011 From: "aloysius bella a aloysius.bella * gmail.com" To: CCL Subject: CCL:G: emission spectra Message-Id: <-44535-110504014741-26565-kAEBiMLp7edpIBtzYlPIgw\a/server.ccl.net> X-Original-From: "aloysius bella a" Date: Wed, 4 May 2011 01:47:37 -0400 Sent to CCL by: "aloysius bella a" [aloysius.bella++gmail.com] Hi all, i am doing tddft calculations for pi conjugated systems to find emission spectra.To study this,i am following the gaussian user reference (http://www.gaussian.com/g_tech/g_ur/k_scrf.htm,) in that,there are 7 steps are given to find emission spectra.I could proceed all the steps that are given for the sample molecule(acetaldehyde). But in my case, i am struggling to proceed the 4th step. I dont know how to modify the torsional angle for my molecule. Is there any thumb rule to perturb the molecule? What should i do to proceed further? Kindly reply. Lot of thanks in advance. A. Bella. aloysius.bella],[gmail.com From owner-chemistry@ccl.net Wed May 4 10:00:00 2011 From: "steinbrt,,rci.rutgers.edu" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44536-110504035330-26076-E89d1liw94YrZPwA/AECLQ:-:server.ccl.net> X-Original-From: steinbrt=rci.rutgers.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 4 May 2011 03:53:21 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: steinbrt(-)rci.rutgers.edu Hi all, On Tue, May 3, 2011 12:53 pm, Jim Kress ccl_nospam++kressworks.com wrote: > Nice try but unresponsive. You can rationalize evil all you want, but it > is still evil. Is evil really the right word to use here? Copyright infringement is certainly a problem for all authors, but as someone who is both producing and using copyrighted works, the lack of some reasonable fair use policy is something that bothers me a lot more. We all agree that publishers need to make a profit, but the 'leave it to the lawyers/MBAs' approach is certainly not the best way to ensure people's access to academic and educational knowledge. Also: Making a copy of a file you own is *not* theft. It can be (and increasingly is these days) against the law, but don't buy the MPAA propaganda of copy=murder. Dr. Thomas Steinbrecher formerly at the BioMaps Institute Rutgers University 610 Taylor Rd. Piscataway, NJ 08854 From owner-chemistry@ccl.net Wed May 4 10:35:00 2011 From: "aloysius bella a aloysius.bella^^^rediffmail.com" To: CCL Subject: CCL:G: emission spectra Message-Id: <-44537-110504014311-22859-72eM4X6LDugVaKI+PJ4vIg#,#server.ccl.net> X-Original-From: "aloysius bella a" Date: Wed, 4 May 2011 01:43:08 -0400 Sent to CCL by: "aloysius bella a" [aloysius.bella-$-rediffmail.com] Hi all, i am doing tddft calculations for pi conjugated systems to find emission spectra.To study this,i am following the gaussian user reference (http://www.gaussian.com/g_tech/g_ur/k_scrf.htm,) in that,there are 7 steps are given to find emission spectra.I could proceed all the steps that are given for the sample molecule(acetaldehyde). But in my case, i am struggling to proceed the 4th step. I dont know how to modify the torsional angle for my molecule. Is there any thumb rule to perturb the molecule? What should i do to proceed further? Kindly reply. Lot of thanks in advance. A. Bella. aloysius.bella * rediffmail.com From owner-chemistry@ccl.net Wed May 4 11:10:00 2011 From: "Jacco van de Streek vandestreek-#-avmatsim.de" To: CCL Subject: CCL: Suggestion needed Message-Id: <-44538-110504083624-31512-pNyWC1sW9ima8J8Rp2H0kQ .. server.ccl.net> X-Original-From: Jacco van de Streek Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 04 May 2011 14:36:12 +0200 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [vandestreek%avmatsim.de] On 05/03/2011 10:05 PM, rocky walden rocky.walden19**gmail.com wrote: > I have performed Geometry optimization of a Crystal structure > download form CCDC database, ( using COMPASS forcefields), When i used > Steeped Descent algorithm with 1000 iterations the out of the > optimization states that it is not converged. I also have choosen the > option to optimize the cell. > But when i performed the same calculation with Conjugate Gradient > algorithm (5000 steps of iterations) the out put did not return the > message Not converged. > > Does the max no.of iterations play any role or do the algorithm? > > As the structure is downloaded form CCDC database it has repeating > units of the molecules. Do this condition plays any role in optimization > process? I thought that COMPASS was a proprietary force field, available only through Accelrys software (a quick Google search suggests that that used to be the case but has changed now?). I think that means that you are using Materials Studio. For the predecessor of Materials Studio, Cerius2, the default minimisation algorithm was the "Smart Minimizer", which uses a series of minimisation algorithms starting with a very robust algorithm and switching to quasi-Newton close to the minimum. In my experience, that was an excellent minimisation algorithm, and switching to other algorithms often led to non-convergence (for the systems I was working on at the time, which had some very soft modes). So my first question would be: do you have a quasi-Newton or a Smart Minimizer option available? If yes: is there any particular reason why you are not using those algorithms? Having "repeating units of molecules", in other words 3D periodic boundary conditions, does of course play a role in general. If hard cut-offs, without splines, are used, atoms can hop into and out of the cut-off radius, which leads to discontinuities. For isolated (small) molecules, this is rarely an issue. Also, the 3D periodicity introduces degrees of freedom not found when a single molecule in vacuum is minimised, like the unit-cell parameters, and translations and rotations of whole molecules. Translations or rotations of whole molecules can be rather soft degrees of freedom compared to e.g. a bond length, with much shallower minima, and this could in principle lead to convergence problems for a crystal structure even if the molecule in vacuum minimises without any problem. However, I would expect Accelrys software to be able to cope with that without any problems (using Ewald summation and splines), certainly when simply a force field is used. Regarding the convergence, you could check if the energy of the structure that has not converged is higher (less favourable) than the energy of the converged structure. Given the speed of computers today, I would expect the software to define a default number of steps that most of the time suffices to lead to convergence for most crystal structures. So another question you should ask yourself is how much the crystal structure distorts. COMPASS is a pretty good force field in my limited experience, and perhaps the actual error is something like a missing or misplaced hydrogen atom in your crystal structure (hydrogen atoms are largely invisible to X-rays, and especially before the 1980s their positions were quite often "guessed" or simply omitted). If there is an error in your model, your incomplete structure will be very far away from what the force field thinks is a reasonable minimum for your (wrong) structure. That will lead to large distortions, large initial forces (which confuse the minimisation algorithm) etc. Such a hopeless minimisation may well take more steps to converge than the programmers had expected based on validation with correct models (which are much closer to the expected minimum). To answer your question "Does the max no.of iterations play any role or do the algorithm?". Obviously, both play an important role: no algorithm will converge if you set the maximum number of iterations to zero, and if the two algorithms were identical, they would not have different names, so they are different and therefore they behave differently with respect to convergence--the whole concept of "one iteration" may be completely different for the two algorithms, and "one iteration" may take only a fraction of a second for one algorithm, but perhaps a full minute for the other. Correspondingly, both may take three minutes to converge, but one algorithm will need only five iterations, the other may need 5,000 iterations (but both take three minutes for the whole minimisation). But somehow, that is a rather obvious answer, so I am not sure if it answers your question. Best wishes, -- Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany From owner-chemistry@ccl.net Wed May 4 11:44:00 2011 From: "arslan ali arslanali1986\a/gmail.com" To: CCL Subject: CCL: calculating G Message-Id: <-44539-110504083612-31342-+cTVjn++Y9EWoRNvyJjFpw{}server.ccl.net> X-Original-From: arslan ali Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 4 May 2011 17:36:02 +0500 MIME-Version: 1.0 Sent to CCL by: arslan ali [arslanali1986*_*gmail.com] hello how can i calcualte Gibbs free energy of charged molecule in spartan. I am not able to find out steps/options for such calcualtions. thanks in advance. Arslan From owner-chemistry@ccl.net Wed May 4 13:44:00 2011 From: "Sujit Kumar Mondal sujitharvard###gmail.com" To: CCL Subject: CCL:G: MO6 Message-Id: <-44540-110504133603-12067-F9VdfwPh6YcOW7NbzhF3MQ=server.ccl.net> X-Original-From: Sujit Kumar Mondal Content-Type: multipart/alternative; boundary=001636ed6a183b902404a276b074 Date: Wed, 4 May 2011 12:35:53 -0500 MIME-Version: 1.0 Sent to CCL by: Sujit Kumar Mondal [sujitharvard[]gmail.com] --001636ed6a183b902404a276b074 Content-Type: text/plain; charset=ISO-8859-1 Thanks to Deepthi Jose and Aloysius Bella for your suggestion. Can anyone suggest me the possible answer regarding to my 2nd question... *"2)# M06/6-311+G(d,p) opt scf=(tight, cdiis) for Fe+3 complex, link died couple of times after 30min of run!! I do not know the reason behind it, though b3lyp gave nice results, anybody can suggest what will be the probable problem for this case?"* i know transition metal generally behaves very funny sometimes..earlier i used the los-almos basis set for (Effective core-potential) Fe+3-complex and it gave some good results but here with M06 i am screwed now!! please suggest me... Sujit On Wed, May 4, 2011 at 12:09 AM, Aloysius Bella aloysius.bella[-] rediffmail.com wrote: > Hi Sujit, > Do check whether you have typed MO6 or M06. You should put M(zero > i.e.,number)6 , not M(O-alphabet)6. try. > regards, > Bella. > On Wed, 04 May 2011 09:35:04 +0530 "Sujit Kumar Mondal sujitharvard### > gmail.com" wrote > > > *Hi all* > *I am sujit, i am working with Gaussian-09 very recently(2months)/ can be > described as a beginnner. I am very much using B3lyp hybrid-function for > verious calculation such geometry opt, IRC, Scrf etc but recently i am > facing problem with MO6 function for IRC calculation!! * > *1)# MO6/6-311+G(d,p) IRC=(calcfc,maxcycle=1000) > scf=(tight,maxcycle=1000,cdiis) showing me all the time* *syntax error!! can > anyone tell me what kind of mistake I am making during my input command in > the route section?* > ** > *2)# MO6/6-311+G(d,p) opt scf=(tight, cdiis) for Fe+3 complex, link died > couple of times after 30min of run!! I do not know the reason behind it, > though b3lyp gave nice results, anybody can suggest what will be the > probable problem for this case?* > > *3)# MO6/6-311+G(d,p) opt=(calcall,maxcycle=600) > scf=(tight,maxcycle=600,cdiis) Also I am having problem for frequency > calculation using MO6, syntax error, please correct my mistake?* > ** > *Looking forward for suggestions* > ** > *Sujit* > ** > ** > > > --001636ed6a183b902404a276b074 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Thanks to Deepthi Jose and Aloysius Bella for = your suggestion. Can anyone suggest me the possible answer regarding to my = 2nd question...=20
"2)# M06/6-311+G(d,p) opt scf=3D(tight, cdiis) for Fe+3 c= omplex,=A0link died couple of times after 30min of run!! I do not know the = reason behind it, though b3lyp gave nice results, =A0anybody can suggest wh= at will be the probable=A0problem for this case?"
=A0
i know transition metal generally behaves very= funny sometimes..earlier i used the los-almos basis set for (Effective cor= e-potential) Fe+3-complex and it gave some good results but here with M06 i= am screwed now!! please suggest me...
=A0
Sujit
=A0
=A0
On Wed, May 4, 2011 at 12:09 AM, Aloysius Bella = aloysius.bella[-]rediffmail.com <owner-chemistry= ,,ccl.net> wrote:
Hi Sujit,
Do check whether yo= u have typed MO6 or M06. You should put M(zero i.e.,number)6 ,=A0 not M(O-a= lphabet)6. try.
regards,
Bella.
On Wed, 04 May 2011 09:35:04 +0530 "Sujit Kumar = Mondal sujitharvard###gmail= .com" <owner-chemistry:-:ccl.net> wrote
>=20
Hi all
I am sujit, i am working with=A0Gaussian-09 very recently(2mon= ths)/ can be described as a beginnner. I am very much using B3lyp hybrid-fu= nction for verious calculation such geometry opt, IRC, Scrf etc but recentl= y i am facing problem with MO6 function for IRC calculation!!
1)# MO6/6-311+G(d,p) IRC=3D(calcfc,maxcycle=3D1000) scf=3D(tig= ht,maxcycle=3D1000,cdiis) showing me all the time syntax error!!=A0can anyone = tell me what kind of mistake I am=A0making during my input command in the r= oute section?
=A0
2)# MO6/6-311+G(d,p) opt scf=3D(tight, cdiis) for Fe+3 complex= ,=A0link died couple of times after 30min of run!! I do not know the reason= behind it, though b3lyp gave nice results, =A0anybody can suggest what wil= l be the probable=A0problem for this case?
=A0
3)# MO6/6-311+G(d,p) opt=3D(calcall,maxcycle=3D600) scf=3D(tig= ht,maxcycle=3D600,cdiis)=A0Also=A0I am having problem for frequency calcula= tion using MO6, syntax error, please correct my mis= take?
=A0
Looking forward for suggestions=
=A0
Sujit
=A0
=A0


--001636ed6a183b902404a276b074-- From owner-chemistry@ccl.net Wed May 4 14:22:00 2011 From: "Jean Jules FIFEN julesfifen{:}gmail.com" To: CCL Subject: CCL:G: MO6 Message-Id: <-44541-110504134806-2780-0FnNboj6xPm4PDFnzvLSRw===server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=bcaec517a9c85e960204a276dbbc Date: Wed, 4 May 2011 18:47:56 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen**gmail.com] --bcaec517a9c85e960204a276dbbc Content-Type: text/plain; charset=ISO-8859-1 Dear Sujit, I think that, for the first and the third problem, you could first of all left down the keyword *maxcycle* and its argument. Moreover, I think it is useless to add the keyword *scf=tight* since it is the default in G09. If this work, try reducing the argument of maxcycle for IRC to 50 or less. For opt calculations, I think that the key word maxcycle is rather *maxcycles* (see the manual). Relevant to the second problem, I am not sure that the Thrular functional M06 is appropriate for metal ions. But, M06-2X is appropriated. After doing this, if the problem is still present, remove the keyword cdiis to allow the program to use a combination of EDIIS and CDIIS. Hope this will help, Best regards, On 4 May 2011 05:33, Deepthi Jose deepthi,iisertvm.ac.in < owner-chemistry%a%ccl.net> wrote: > Dear Sujit, > The functional is M06 (MZeroSix) not MO6. > > > > Regards > Deepthi > > > On Wed, May 4, 2011 at 5:05 AM, Sujit Kumar Mondal sujitharvard### > gmail.com wrote: > >> *Hi all* >> *I am sujit, i am working with Gaussian-09 very recently(2months)/ can be >> described as a beginnner. I am very much using B3lyp hybrid-function for >> verious calculation such geometry opt, IRC, Scrf etc but recently i am >> facing problem with MO6 function for IRC calculation!! * >> *1)# MO6/6-311+G(d,p) IRC=(calcfc,maxcycle=1000) >> scf=(tight,maxcycle=1000,cdiis) showing me all the time* *syntax error!! can >> anyone tell me what kind of mistake I am making during my input command in >> the route section?* >> ** >> *2)# MO6/6-311+G(d,p) opt scf=(tight, cdiis) for Fe+3 complex, link died >> couple of times after 30min of run!! I do not know the reason behind it, >> though b3lyp gave nice results, anybody can suggest what will be the >> probable problem for this case?* >> >> *3)# MO6/6-311+G(d,p) opt=(calcall,maxcycle=600) >> scf=(tight,maxcycle=600,cdiis) Also I am having problem for frequency >> calculation using MO6, syntax error, please correct my mistake?* >> ** >> *Looking forward for suggestions* >> ** >> *Sujit* >> ** >> ** >> > > -- Jean Jules FIFEN. University of Douala Faculty of Science Laboratoire de Physique Fondamentale. --bcaec517a9c85e960204a276dbbc Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sujit,
I think that,
for the first and the third problem, you co= uld first of all left down the keyword maxcycle and its argument.=A0= Moreover, I think it is useless to add the keyword scf=3Dtight sinc= e it is the default in G09. If this work, try reducing the argument of maxc= ycle for IRC to 50 or less. For opt calculations, I think that the key word= maxcycle is rather maxcycles (see the manual).
Relevant to the second problem, I am not sure that the Thrular functional M= 06 is appropriate for metal ions. But, M06-2X is appropriated.
After doi= ng this, if the problem is still present, remove the keyword cdiis to allow= the program to use a combination of EDIIS and CDIIS.
Hope this will help,

Best regards,

On 4 May 2011 05:33, Deepthi Jose deepthi,iisertvm.ac.in <owner-chemistry%a%ccl.net> wrote:
Dear Sujit,
Th= e functional is M06 (MZeroSix) not MO6.



Regards
Deepthi


On Wed, May= 4, 2011 at 5:05 AM, Sujit Kumar Mondal sujitharvard###gmail.com <owner-che= mistry###ccl.net> wrote:
Hi all
I am sujit, i am working with=A0Gaussian-09 very recently(2months)/= can be described as a beginnner. I am very much using B3lyp hybrid-functio= n for verious calculation such geometry opt, IRC, Scrf etc but recently i a= m facing problem with MO6 function for IRC calculation!!
1)# MO6/6-311+G(d,p) IRC=3D(calcfc,maxcycle=3D1000) scf=3D(tight,ma= xcycle=3D1000,cdiis) showing me all the time syntax error!!=A0can anyone tell me what ki= nd of mistake I am=A0making during my input command in the route section?
=A0
2)# MO6/6-311+G(d,p) opt scf=3D(tight, cdiis) for Fe+3 complex,=A0l= ink died couple of times after 30min of run!! I do not know the reason behi= nd it, though b3lyp gave nice results, =A0anybody can suggest what will be = the probable=A0problem for this case?
=A0
3)# MO6/6-311+G(d,p) opt=3D(calcall,maxcycle=3D600) scf=3D(tight,ma= xcycle=3D600,cdiis)=A0Also=A0I am having problem for frequency calculation = using MO6, syntax error, please correct my mistake?=
=A0
Looking forward for suggestions<= /div>
=A0
Sujit
=A0
=A0




--
Jean Jules= FIFEN.
University of Douala
Faculty of Science
Laboratoire de Phy= sique Fondamentale.

--bcaec517a9c85e960204a276dbbc-- From owner-chemistry@ccl.net Wed May 4 15:20:01 2011 From: "Hao-Bo Guo guohaobo/a\gmail.com" To: CCL Subject: CCL:G: MO6 Message-Id: <-44542-110504150840-32054-ZYTHldgG3BcBP2czlrZ18Q]|[server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/alternative; boundary=20cf307ca0449359bc04a277fba8 Date: Wed, 4 May 2011 15:08:32 -0400 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo() gmail.com] --20cf307ca0449359bc04a277fba8 Content-Type: text/plain; charset=ISO-8859-1 I do not know where exactly your job failed. But if the link died at the scf iterations, you may try scf=qc, and for convergence problem you may try iop(5/13=1). Hao-Bo Guo On Wed, May 4, 2011 at 1:35 PM, Sujit Kumar Mondal sujitharvard###gmail.com wrote: > Thanks to Deepthi Jose and Aloysius Bella for your suggestion. Can anyone > suggest me the possible answer regarding to my 2nd question... > *"2)# M06/6-311+G(d,p) opt scf=(tight, cdiis) for Fe+3 complex, link died > couple of times after 30min of run!! I do not know the reason behind it, > though b3lyp gave nice results, anybody can suggest what will be the > probable problem for this case?"* > > i know transition metal generally behaves very funny sometimes..earlier i > used the los-almos basis set for (Effective core-potential) Fe+3-complex and > it gave some good results but here with M06 i am screwed now!! please > suggest me... > > Sujit > > > On Wed, May 4, 2011 at 12:09 AM, Aloysius Bella aloysius.bella[-] > rediffmail.com wrote: > >> Hi Sujit, >> Do check whether you have typed MO6 or M06. You should put M(zero >> i.e.,number)6 , not M(O-alphabet)6. try. >> regards, >> Bella. >> On Wed, 04 May 2011 09:35:04 +0530 "Sujit Kumar Mondal sujitharvard### >> gmail.com" wrote >> > >> *Hi all* >> *I am sujit, i am working with Gaussian-09 very recently(2months)/ can be >> described as a beginnner. I am very much using B3lyp hybrid-function for >> verious calculation such geometry opt, IRC, Scrf etc but recently i am >> facing problem with MO6 function for IRC calculation!! * >> *1)# MO6/6-311+G(d,p) IRC=(calcfc,maxcycle=1000) >> scf=(tight,maxcycle=1000,cdiis) showing me all the time* *syntax error!! can >> anyone tell me what kind of mistake I am making during my input command in >> the route section?* >> ** >> *2)# MO6/6-311+G(d,p) opt scf=(tight, cdiis) for Fe+3 complex, link died >> couple of times after 30min of run!! I do not know the reason behind it, >> though b3lyp gave nice results, anybody can suggest what will be the >> probable problem for this case?* >> >> *3)# MO6/6-311+G(d,p) opt=(calcall,maxcycle=600) >> scf=(tight,maxcycle=600,cdiis) Also I am having problem for frequency >> calculation using MO6, syntax error, please correct my mistake?* >> ** >> *Looking forward for suggestions* >> ** >> *Sujit* >> ** >> ** >> >> >> > > > --20cf307ca0449359bc04a277fba8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I do not know where exactly your job failed. But if the link died at the sc= f iterations, you may try scf=3Dqc, and for convergence problem you may try= iop(5/13=3D1).

Hao-Bo Guo

On Wed,= May 4, 2011 at 1:35 PM, Sujit Kumar Mondal sujitharvard###gmail.com <owner-chemistry-.-ccl.net> wrote:
Thanks to Deepthi Jose and Aloysius Bella for your suggestion.= Can anyone suggest me the possible answer regarding to my 2nd question...<= /font>=20
"2)# M06/6-311+G(d,p) opt scf=3D(tight, cdiis) for Fe+3 comple= x,=A0link died couple of times after 30min of run!! I do not know the reaso= n behind it, though b3lyp gave nice results, =A0anybody can suggest what wi= ll be the probable=A0problem for this case?"
=A0
i know transition metal generally behaves very= funny sometimes..earlier i used the los-almos basis set for (Effective cor= e-potential) Fe+3-complex and it gave some good results but here with M06 i= am screwed now!! please suggest me...
=A0
Sujit
=A0
=A0
On Wed, May 4, 2011 at 12:09 AM, Aloysius Bella = aloysius.bella[-]rediff= mail.com <owner-chemistry#%#ccl.net> wrote:
Hi Sujit,
Do c= heck whether you have typed MO6 or M06. You should put M(zero i.e.,number)6= ,=A0 not M(O-alphabet)6. try.
regards,
Bella.
On Wed, 04 May 2011 09:35:04 +0530 "Sujit Kumar = Mondal sujitharvard###gmail= .com" <owner-chemistry:-:ccl.net> wrote
>=20
Hi all
I am sujit, i am working with=A0Gaussian-09 very recently(2months)/= can be described as a beginnner. I am very much using B3lyp hybrid-functio= n for verious calculation such geometry opt, IRC, Scrf etc but recently i a= m facing problem with MO6 function for IRC calculation!!
1)# MO6/6-311+G(d,p) IRC=3D(calcfc,maxcycle=3D1000) scf=3D(tight,ma= xcycle=3D1000,cdiis) showing me all the time syntax error!!=A0can anyone tell me what ki= nd of mistake I am=A0making during my input command in the route section?
=A0
2)# MO6/6-311+G(d,p) opt scf=3D(tight, cdiis) for Fe+3 complex,=A0l= ink died couple of times after 30min of run!! I do not know the reason behi= nd it, though b3lyp gave nice results, =A0anybody can suggest what will be = the probable=A0problem for this case?
=A0
3)# MO6/6-311+G(d,p) opt=3D(calcall,maxcycle=3D600) scf=3D(tight,ma= xcycle=3D600,cdiis)=A0Also=A0I am having problem for frequency calculation = using MO6, syntax error, please correct my mistake?=
=A0
Looking forward for suggestions<= /div>
=A0
Sujit
=A0
=A0



--20cf307ca0449359bc04a277fba8-- From owner-chemistry@ccl.net Wed May 4 16:35:00 2011 From: "Arun Kumar Subramanian aksub007 ~ gmail.com" To: CCL Subject: CCL: is it possible to do a restrained docking in autodock or autodock vina? Message-Id: <-44543-110504163245-14819-i+ihP0hhJRRkf1v2wnQMtw[-]server.ccl.net> X-Original-From: Arun Kumar Subramanian Content-Type: multipart/alternative; boundary=20cf303b431b4441b704a2792885 Date: Wed, 4 May 2011 13:32:17 -0700 MIME-Version: 1.0 Sent to CCL by: Arun Kumar Subramanian [aksub007]![gmail.com] --20cf303b431b4441b704a2792885 Content-Type: text/plain; charset=ISO-8859-1 Hi CCLers, I am trying to dock a modified FAD cofactor into a crystallographically known binding pocket using Autodock4. As I am also trying to dock an intermediate structure of a reaction, I am interested in using geometric constraints (it can be a distant constraint or tethering a part of the flexible molecule to tie it to its actual position). The Autodock manual doesnt say if it can do a restrained docking. It will be a great help to know if it is possible in autodock (and autodock vina) or not possible. Also I would appreciate if you can give information about any freeware docking tool that can do a restrained dock. Thanks a lot, in anticipation. Sincerely, ArunKumar. S. --20cf303b431b4441b704a2792885 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi CCLers,

I am trying to dock a modified FAD cofactor i= nto a crystallographically known binding pocket using Autodock4.=A0

As I am also trying to dock an intermediate structure of = a reaction, I am interested in using geometric constraints (it can be a dis= tant constraint or tethering a part of the flexible molecule to tie it to i= ts actual position). The Autodock manual doesnt say if it can do a restrain= ed docking. It will be a great help to know if it is possible in autodock (= and autodock vina) or not possible. Also I would appreciate if you can give= information about any freeware docking tool that can do a restrained dock.=

Thanks a lot, in anticipation.

Sincerely,




ArunKumar. S.
--20cf303b431b4441b704a2792885-- From owner-chemistry@ccl.net Wed May 4 18:42:01 2011 From: "Sujit Kumar Mondal sujitharvard[]gmail.com" To: CCL Subject: CCL:G: MO6 Message-Id: <-44544-110504180855-32161-20hY+0ZOP1ErgpxuDagbmA\a/server.ccl.net> X-Original-From: Sujit Kumar Mondal Content-Type: multipart/alternative; boundary=001636ed6a18ca723c04a27a7f7f Date: Wed, 4 May 2011 17:08:40 -0500 MIME-Version: 1.0 Sent to CCL by: Sujit Kumar Mondal [sujitharvard-.-gmail.com] --001636ed6a18ca723c04a27a7f7f Content-Type: text/plain; charset=ISO-8859-1 Thanks. Sujit On Wed, May 4, 2011 at 2:08 PM, Hao-Bo Guo guohaobo/agmail.com < owner-chemistry*ccl.net> wrote: > I do not know where exactly your job failed. But if the link died at the > scf iterations, you may try scf=qc, and for convergence problem you may try > iop(5/13=1). > > Hao-Bo Guo > > On Wed, May 4, 2011 at 1:35 PM, Sujit Kumar Mondal sujitharvard### > gmail.com wrote: > >> Thanks to Deepthi Jose and Aloysius Bella for your suggestion. Can >> anyone suggest me the possible answer regarding to my 2nd question... >> *"2)# M06/6-311+G(d,p) opt scf=(tight, cdiis) for Fe+3 complex, link died >> couple of times after 30min of run!! I do not know the reason behind it, >> though b3lyp gave nice results, anybody can suggest what will be the >> probable problem for this case?"* >> >> i know transition metal generally behaves very funny sometimes..earlier i >> used the los-almos basis set for (Effective core-potential) Fe+3-complex and >> it gave some good results but here with M06 i am screwed now!! please >> suggest me... >> >> Sujit >> >> >> On Wed, May 4, 2011 at 12:09 AM, Aloysius Bella aloysius.bella[-] >> rediffmail.com wrote: >> >>> Hi Sujit, >>> Do check whether you have typed MO6 or M06. You should put M(zero >>> i.e.,number)6 , not M(O-alphabet)6. try. >>> regards, >>> Bella. >>> On Wed, 04 May 2011 09:35:04 +0530 "Sujit Kumar Mondal sujitharvard### >>> gmail.com" wrote >>> >>> > >>> *Hi all* >>> *I am sujit, i am working with Gaussian-09 very recently(2months)/ can >>> be described as a beginnner. I am very much using B3lyp hybrid-function for >>> verious calculation such geometry opt, IRC, Scrf etc but recently i am >>> facing problem with MO6 function for IRC calculation!! * >>> *1)# MO6/6-311+G(d,p) IRC=(calcfc,maxcycle=1000) >>> scf=(tight,maxcycle=1000,cdiis) showing me all the time* *syntax >>> error!! can anyone tell me what kind of mistake I am making during my >>> input command in the route section?* >>> ** >>> *2)# MO6/6-311+G(d,p) opt scf=(tight, cdiis) for Fe+3 complex, link died >>> couple of times after 30min of run!! I do not know the reason behind it, >>> though b3lyp gave nice results, anybody can suggest what will be the >>> probable problem for this case?* >>> >>> *3)# MO6/6-311+G(d,p) opt=(calcall,maxcycle=600) >>> scf=(tight,maxcycle=600,cdiis) Also I am having problem for frequency >>> calculation using MO6, syntax error, please correct my mistake?* >>> ** >>> *Looking forward for suggestions* >>> ** >>> *Sujit* >>> ** >>> ** >>> >>> >>> >>> >> >> > --001636ed6a18ca723c04a27a7f7f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Thanks.
Sujit

On Wed, May 4, 2011 at 2:08 PM, Hao-Bo Guo guoha= obo/agmail.com <owner-chemistry*ccl.net> wrote:
I do not know where exactly your= job failed. But if the link died at the scf iterations, you may try scf=3D= qc, and for convergence problem you may try iop(5/13=3D1).

Hao-Bo Guo

On Wed, May 4, 2011 at 1:35 PM, Sujit Kumar Mondal sujith= arvard###gmail.com <owner-chemistry*ccl.net> wrote:
Thanks to Deepthi Jose and Aloysius Bella for = your suggestion. Can anyone suggest me the possible answer regarding to my = 2nd question...=20
"2)# M06/6-311+G(d,p) opt scf=3D(tight, cdiis) for Fe+3 comple= x,=A0link died couple of times after 30min of run!! I do not know the reaso= n behind it, though b3lyp gave nice results, =A0anybody can suggest what wi= ll be the probable=A0problem for this case?"
=A0
i know transition metal generally behaves very= funny sometimes..earlier i used the los-almos basis set for (Effective cor= e-potential) Fe+3-complex and it gave some good results but here with M06 i= am screwed now!! please suggest me...
=A0
Sujit
=A0
=A0
On Wed, May 4, 2011 at 12:09 AM, Aloysius Bella aloysius.= bella[-]rediffmail.com= <owner-chemistry#%#ccl.net> wrot= e:
Hi Sujit,
Do check whether you have typed MO6 or M06. = You should put M(zero i.e.,number)6 ,=A0 not M(O-alphabet)6. try.
regard= s,
Bella.
On Wed, 04 May 2011 09:35:04 +0530 "Sujit Kumar = Mondal sujitharvard###gmail= .com" <owner-chemistry:-:ccl.net> wrote=20

>=20
Hi all
I am sujit, i am working with=A0Gaussian-09 very recently(2months)/= can be described as a beginnner. I am very much using B3lyp hybrid-functio= n for verious calculation such geometry opt, IRC, Scrf etc but recently i a= m facing problem with MO6 function for IRC calculation!!
1)# MO6/6-311+G(d,p) IRC=3D(calcfc,maxcycle=3D1000) scf=3D(tight,ma= xcycle=3D1000,cdiis) showing me all the time syntax error!!=A0can anyone tell me what ki= nd of mistake I am=A0making during my input command in the route section?
=A0
2)# MO6/6-311+G(d,p) opt scf=3D(tight, cdiis) for Fe+3 complex,=A0l= ink died couple of times after 30min of run!! I do not know the reason behi= nd it, though b3lyp gave nice results, =A0anybody can suggest what will be = the probable=A0problem for this case?
=A0
3)# MO6/6-311+G(d,p) opt=3D(calcall,maxcycle=3D600) scf=3D(tight,ma= xcycle=3D600,cdiis)=A0Also=A0I am having problem for frequency calculation = using MO6, syntax error, please correct my mistake?=
=A0
Looking forward for suggestions<= /div>
=A0
Sujit
=A0
=A0




--001636ed6a18ca723c04a27a7f7f--