From owner-chemistry@ccl.net Wed Feb 10 04:26:01 2010 From: "sina rastegar sina_rastegar1979(_)yahoo.com" To: CCL Subject: CCL: optimaization problem Message-Id: <-41228-100210041548-11993-+gEolFXpKDC4Q7iroNOiTg{=}server.ccl.net> X-Original-From: "sina rastegar" Date: Wed, 10 Feb 2010 04:15:42 -0500 Sent to CCL by: "sina rastegar" [sina_rastegar1979|yahoo.com] I want to optimize a cluster of carbon (c48b12) with calcium which is dopped in a pentagonal surface.after i want to study the absorption of hydrogen molecule.I use oniom.this is my route section. oniom(umpw1pw91/6-31+g(d):ub3lyp/3-21g) but unfortunately i have the error of link 1502 and when i use scf=qc the error will be 1508. this is my z-matrix. B 0 1.59211359 -1.77002419 -2.61421226 L C 0 2.32007659 -0.42245019 -2.45354626 L H 5 0.0000 C 0 1.61061859 -2.70944519 -1.45756526 L C 0 0.24659959 -1.45145819 -3.32198626 L C 0 3.07117559 -0.17752519 -1.27240726 H C 0 2.36795359 -2.40855519 -0.25303726 L H 11 0.0000 C 0 0.23921059 -0.06605419 -3.61188626 L C 0 1.45510759 0.61075581 -3.05651726 L C 0 0.35707459 -3.38759419 -1.08295626 L C 0 -0.95311842 -2.11455419 -2.88209026 L C 0 3.03273559 -1.16354019 -0.15060126 H C 0 1.31415659 1.90652981 -2.51624826 L B 0 2.89503459 1.19357081 -0.63231126 H B 0 1.58023459 -3.06929719 0.94888874 L C 0 0.34942559 -3.74587619 0.30336974 L C 0 -0.88554542 -3.07249119 -1.79226926 L B 0 -1.08762142 0.69131181 -3.55927026 L C 0 -2.27557042 -1.41191619 -2.85137026 L C 0 3.07970459 -0.44186919 1.15732274 H C 0 1.49556959 -2.30580519 2.28910775 L C 0 -2.34964642 -0.05695819 -3.12802226 L B 0 -3.06258041 -1.99349719 -1.67510526 L C 0 -2.17984942 -3.06539319 -1.03698526 L B 0 -0.92235941 -3.58292319 1.08779274 L C 0 2.97281059 1.01496581 0.88998374 H C 0 -1.15007042 2.07139680 -2.90723626 L C 0 0.02237759 2.66967081 -2.48710826 L C 0 2.04434459 2.25677481 -1.28713826 L H 13 0.0000 B 0 2.31720659 -0.98462819 2.36680774 L H 19 0.0000 C 0 -2.22589442 -3.22579819 0.33373974 L C 0 -0.96854141 -2.70965219 2.39456174 L C 0 0.24618259 -2.05174419 2.91341274 L C 0 1.32005659 3.14493581 -0.44904926 L B 0 0.00476559 3.54448981 -1.20952226 L C 0 -3.85729241 -1.04218819 -0.77596526 L C 0 -3.10186242 0.84924681 -2.21383626 L C 0 -2.39761542 2.11879781 -2.07600126 L C 0 2.17568060 1.86072081 1.68211974 L H 25 0.0000 C 0 0.20653659 -0.66109019 3.51366175 L C 0 1.47574459 0.02273882 3.17063974 L C 0 1.45101559 1.37821082 2.85665374 L C 0 1.35240359 2.96153181 1.01284174 L C 0 -1.29150841 3.70517881 -0.47049726 L C 0 -2.41078141 2.91488681 -0.86132726 L C 0 -2.21927141 -2.05727119 2.42885074 L C 0 -3.01503441 -2.29171719 1.20042374 L C 0 -3.80804841 -1.24783919 0.69354774 L C 0 -3.88493741 0.33663681 -1.11721726 L C 0 -1.01343041 0.00072982 3.61210475 L B 0 0.13931859 2.19189982 2.92181074 L C 0 0.19340659 3.23892881 1.76539574 L B 0 -1.16219841 3.52383981 1.07494874 L B 0 -2.29952441 -0.69073419 3.11476474 L C 0 -3.15269041 2.41003081 0.33865474 L B 0 -3.94326541 1.13349280 0.19951774 L C 0 -3.88514441 0.09581181 1.34548774 L C 0 -1.15190841 1.42928382 3.27225774 L C 0 -2.42292541 2.66860381 1.52103474 L C 0 -3.17128441 0.40585881 2.48846774 L C 0 -2.39444841 1.67239182 2.57674874 L Ca 0 5.27556659 0.06675381 0.06250874 H H 0 7.27497981 0.09419747 0.02258868 H H 0 7.87497981 0.09419747 0.02258868 H From owner-chemistry@ccl.net Wed Feb 10 04:58:00 2010 From: "Prasenjit SEAL prasenjit.seal[-]crm2.uhp-nancy.fr" To: CCL Subject: CCL: Generating a charge density file using MOLPRO Message-Id: <-41229-100210034410-7863-UNCu3teik5eooyGJba7PJg_+_server.ccl.net> X-Original-From: Prasenjit SEAL Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 10 Feb 2010 09:43:56 +0100 MIME-Version: 1.0 Sent to CCL by: Prasenjit SEAL [prasenjit.seal[#]crm2.uhp-nancy.fr] Hello CCL users, Can anyone tell me how to generate a cube file or the charge density file using MOLPRO software? Best regards, Prasenjit From owner-chemistry@ccl.net Wed Feb 10 06:03:00 2010 From: "rinu iyer rinuiyer : gmail.com" To: CCL Subject: CCL: optimaization problem Message-Id: <-41230-100210060052-8768-WLlGBxvHT6TfP8CDsCn3jw*server.ccl.net> X-Original-From: rinu iyer Content-Type: multipart/alternative; boundary=0016e6407f0e81e136047f3cf14a Date: Wed, 10 Feb 2010 16:30:33 +0530 MIME-Version: 1.0 Sent to CCL by: rinu iyer [rinuiyer=-=gmail.com] --0016e6407f0e81e136047f3cf14a Content-Type: text/plain; charset=ISO-8859-1 Specify more memory in .inp (*%mem*=*N*mb). Possibly, also increase *pvmem*value in run script. Especially solvent calculations can exhibit allocation failures and explicit amounts of memory should be specified. -- K.R.Ramya Research fellow IIndian Institute of Science Education & Research(IISER) Central Tower, Sai Trinity Building, Sutarwadi Road, Pashan, Pune 411021, INDIA --0016e6407f0e81e136047f3cf14a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Specify more memory in .inp (%mem=3DNmb).= Possibly, also increase pvmem value in run script. Especially solvent calculations can exhibit allocation failures and=A0explicit amounts of=A0memory should be specified.=
--
K.R.Ramya
Research fellow
IIndian Institute of Science Edu= cation & Research(IISER)
Central Tower, Sai Trinity Building, Sutarw= adi Road, Pashan,
Pune 411021, INDIA
--0016e6407f0e81e136047f3cf14a-- From owner-chemistry@ccl.net Wed Feb 10 09:28:00 2010 From: "John john- -ccdc.cam.ac.uk" To: CCL Subject: CCL: I have a question for you all Message-Id: <-41231-100210063809-26220-6pHpHtpOYFe8DRe/sX48wA##server.ccl.net> X-Original-From: "John" Content-Language: en-gb Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01CAAA45.7DB35310" Date: Wed, 10 Feb 2010 11:37:57 -0000 MIME-Version: 1.0 Sent to CCL by: "John" [john*o*ccdc.cam.ac.uk] This is a multi-part message in MIME format. ------=_NextPart_000_0001_01CAAA45.7DB35310 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi Rocky, I would just like to point out that computational methods are not your only resource when considering which conformers are energetically available to a structure. The Cambridge Structural Database contains experimentally determined structures for many commonly occurring carbon containing motifs (over 500,000 structures in all) and you may therein be able to find information on the preferred conformations for those that are interesting to you. If your academic department already has a licence to the Cambridge Structural Database System then you should be able to access it via a Windows interface at no charge. For more information please see: http://www.ccdc.cam.ac.uk/products/csd/ http://www.ccdc.cam.ac.uk/products/csd_system/ regards John Liebeschuetz - Cambridge Crystallographic Data Centre > From: owner-chemistry+ccdc-announce==ccdc.cam.ac.uk:+:ccl.net [mailto:owner-chemistry+ccdc-announce==ccdc.cam.ac.uk:+:ccl.net] On Behalf Of rocky walden rocky.walden19..gmail.com Sent: 09 February 2010 16:59 To: Rutland, Anne Subject: CCL: I have a question for you all Hiii People, I usually have lot of questions in my mind. The question that worries me is this thing How can we predict the Conformational energies of Cis Trans isomers in Cyclohexane using computational tools? By the energy values only we are able to tell whether Cis or trans isomer is stable. Let me know if there is any special techniques or theory appliccable. Is there any computational tool that does this work (free tool only Windows Version is preferable). Cheers rocky ROCKY !!! ROCKS LEGAL NOTICE Unless expressly stated otherwise, information contained in this message is confidential. If this message is not intended for you, please inform postmaster:+:ccdc.cam.ac.uk and delete the message. The Cambridge Crystallographic Data Centre is a company Limited by Guarantee and a Registered Charity. Registered in England No. 2155347 Registered Charity No. 800579 Registered office 12 Union Road, Cambridge CB2 1EZ. ------=_NextPart_000_0001_01CAAA45.7DB35310 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

 

Hi Rocky,

       &nbs= p;     I would just like to point out that computational methods are not = your only resource when considering which conformers are energetically = available to a structure. The Cambridge Structural Database contains experimentally determined structures for many commonly occurring carbon containing = motifs (over 500,000 structures in all)  and you may therein be able to = find information on the preferred conformations for those that are = interesting to you. If your academic department already has a licence  to the Cambridge Structural = Database System  then you should be able to = access it via a Windows interface at no charge.

 

       &nbs= p; For more information please see:

 

http://www.ccdc.cam.ac.uk/products/csd/<= /span>

http://www.ccdc.c= am.ac.uk/products/csd_system/

 

       &nbs= p;            = ;        regards

 

       &nbs= p;            = ;            =          John  Liebeschuetz  -  Cambridge Crystallographic Data = Centre

 

From:<= font size=3D2 face=3DTahoma> owner-chemistry+ccdc-announce=3D=3Dccdc.cam.ac.uk:+:ccl.net = [mailto:owner-chemistry+ccdc-announce=3D=3Dccdc.cam.ac.uk:+:ccl.net] On Behalf Of rocky walden rocky.walden19..gmail.com
Sent: 09 February 2010 = 16:59
To: Rutland, Anne =
Subject: CCL: I have a = question for you all

 

Hiii People,
  I usually have lot of questions in my mind. The question that = worries me is this thing
 How can we predict the Conformational energies of Cis Trans = isomers in Cyclohexane using computational tools?
 By the energy values only we are able to tell whether Cis or trans = isomer is stable.
 Let me know if there is any special techniques or theory = appliccable.
 Is there any computational tool that does this work (free tool = only Windows Version is preferable).

Cheers
rocky
ROCKY !!! ROCKS

------=_NextPart_000_0001_01CAAA45.7DB35310-- From owner-chemistry@ccl.net Wed Feb 10 10:03:00 2010 From: "jaleel uc jaleel.uc/a\gmail.com" To: CCL Subject: CCL: I have a question for you all Message-Id: <-41232-100209234639-14636-JIdpgD4bppdQ1eQhLJj+kA|,|server.ccl.net> X-Original-From: jaleel uc Content-Type: multipart/alternative; boundary=0016369208a79b3916047f379d03 Date: Wed, 10 Feb 2010 10:09:10 +0530 MIME-Version: 1.0 Sent to CCL by: jaleel uc [jaleel.uc_+_gmail.com] --0016369208a79b3916047f379d03 Content-Type: text/plain; charset=ISO-8859-1 Dear sir It possible . Please refer the hyper chem Manuel for this the same problem is solved in their Manual values are Energy Chair 1.33 Boat 8.31 for computational chem please refer the http://www.hyper.com/ On 2/9/10, rocky walden rocky.walden19..gmail.com wrote: > > Hiii People, > I usually have lot of questions in my mind. The question that worries me > is this thing > How can we predict the Conformational energies of Cis Trans isomers in > Cyclohexane using computational tools? > By the energy values only we are able to tell whether Cis or trans isomer > is stable. > Let me know if there is any special techniques or theory appliccable. > Is there any computational tool that does this work (free tool only > Windows Version is preferable). > > Cheers > rocky > ROCKY !!! ROCKS > -- Dr U.C.A.Jaleel. lecturer in cheminformatics Malabar christian college calicut --0016369208a79b3916047f379d03 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear sir
=A0
It possible . Please refer the hyper chem Manue= l for this the same problem is solved in their Manual values are
=A0
Energy=A0=A0=A0 =A0Chair =A01.33
=A0
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0= =A0=A0=A0Boat=A0 =A08.31
=A0
for =A0computational chem please refer the http://www.hype= r.com/

=A0
On 2/9/10, r= ocky walden rocky.walden19..gmail.com = <owner-chemistry[a]ccl.net&= gt; wrote:
Hiii People,
=A0 I usually ha= ve lot of questions in my mind. The question that worries me is this thing<= br> =A0How can we predict the Conformational energies of Cis Trans isomers in C= yclohexane using computational tools?
=A0By the energy values only we ar= e able to tell whether Cis or trans isomer is stable.
=A0Let me know if = there is any special techniques or theory appliccable.
=A0Is there any computational tool that does this work (free tool only Wind= ows Version is preferable).

Cheers
rocky
ROCKY !!! ROCKS



--
Dr U.C.A.Jaleel.
lectu= rer in cheminformatics
Malabar christian college
calicut=20 --0016369208a79b3916047f379d03-- From owner-chemistry@ccl.net Wed Feb 10 10:48:01 2010 From: "Matthew Clark mclark===pharmatrope.com" To: CCL Subject: CCL: I have a question for you all Message-Id: <-41233-100210100109-2990-KfWDD30Xx/DNBQNADrfKhA(0)server.ccl.net> X-Original-From: Matthew Clark Content-Type: multipart/alternative; boundary="=-zr3Lkh/sxNfr6ArS8jgU" Date: Wed, 10 Feb 2010 10:00:56 -0500 Mime-Version: 1.0 Sent to CCL by: Matthew Clark [mclark[A]pharmatrope.com] --=-zr3Lkh/sxNfr6ArS8jgU Content-Type: text/plain Content-Transfer-Encoding: 7bit The MM2/3 programs are parametrized to be especially good at those kinds of conformational energy differences, although many other molecular mechanics programs also give good answers. Matt On Tue, 2010-02-09 at 22:28 +0530, rocky walden rocky.walden19..gmail.com wrote: > Hiii People, > I usually have lot of questions in my mind. The question that > worries me is this thing > How can we predict the Conformational energies of Cis Trans isomers > in Cyclohexane using computational tools? > By the energy values only we are able to tell whether Cis or trans > isomer is stable. > Let me know if there is any special techniques or theory appliccable. > Is there any computational tool that does this work (free tool only > Windows Version is preferable). > > Cheers > rocky > ROCKY !!! ROCKS ________________________________________________________________________ Matthew Clark, Ph. D. CIO Pharmatrope Ltd 610 772 4652 mclark^^pharmatrope.com --=-zr3Lkh/sxNfr6ArS8jgU Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 7bit
The MM2/3 programs are parametrized to be especially good at those kinds of conformational energy differences, although many other molecular mechanics programs also give good answers.

Matt


On Tue, 2010-02-09 at 22:28 +0530, rocky walden rocky.walden19..gmail.com wrote:
Hiii People,
  I usually have lot of questions in my mind. The question that worries me is this thing
 How can we predict the Conformational energies of Cis Trans isomers in Cyclohexane using computational tools?
 By the energy values only we are able to tell whether Cis or trans isomer is stable.
 Let me know if there is any special techniques or theory appliccable.
 Is there any computational tool that does this work (free tool only Windows Version is preferable).

Cheers
rocky
ROCKY !!! ROCKS




Matthew Clark, Ph. D.
CIO Pharmatrope Ltd
610 772 4652
mclark^^pharmatrope.com
--=-zr3Lkh/sxNfr6ArS8jgU-- From owner-chemistry@ccl.net Wed Feb 10 12:16:00 2010 From: "Igor Filippov igor.v.filippov\a/gmail.com" To: CCL Subject: CCL:G: I have a question for you all Message-Id: <-41234-100210011945-5848-UGDCcJVilowrepIFmAWPkQ||server.ccl.net> X-Original-From: Igor Filippov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 10 Feb 2010 00:25:15 -0500 Mime-Version: 1.0 Sent to CCL by: Igor Filippov [igor.v.filippov-*-gmail.com] I have to say I agree with Gonzalo on this point. While everyone is welcome to ask questions, beginning the request with "Hiii People", and signing it with "ROCKY!!! ROCKS" seems to me (and I could be in the minority on that) a sign of disrespect, pure and simple. If one is requesting assistance of busy professionals a little courtesy can go a long way. I am always happy to help everyone with the problems with software I've developed or familiar with, but there are a few simple things that I implicitly expect from the person asking a question: 1) Please be polite. We are not being paid to answer (or even read) your questions. 2) Please sign your email. It does not have to be a real name, but seeing signature such as "ROCKY!!! ROCKS" or "Blue Power" or some other freshman-style nickname makes me feel disrespected. 3) Please do at least a minimum of research (google search? wikipedia? anything...) before posting a question. If you cannot be bothered to type a few words in google why should anyone bother to reply to you? Now, this is just my ideas, nobody has to follow or even care about them. On the other hand I read Mr. ROCKY!!! ROCKS question only after seeing the messages from Gonzalo and Zoran, otherwise it would not even register on my radar with the greeting such as "Hiii People". I am only writing this because I'm unfortunately seeing more messages such as this and it saddens me if this is beginning to be accepted as the norm. Just my two cents, Igor On Tue, 2010-02-09 at 18:54 -0500, zoran matovic zmatovic : kg.ac.rs wrote: > Sent to CCL by: "zoran matovic" [zmatovic*_*kg.ac.rs] > Hello CCL's users, > > I have red Gonzalo's reply to "rocky" and (as before to similar debate) have > a moderate attitude. May be Rocky has something else on his mind putting > quest like this, may be he is young may be senior researcher may be > unexperienced but has the right to ask for answer. His quest might be > considered by computational chemists as silly one, wasting of e-mail space, > a quest of one who did not read none of chemistry or comp chem literature or > manuals or web pages, but he has the right to ask (this is free forum for > everyone) and we may answer to or not to answer. > > Well, as far as we consider calcs of cis and trans conformational energies > of substituted cyclohexanes there are plenty of literature and web pages (as > Gonzalo said) and only what Rocky has to do is to: google or find wikipedia > for the next words: conformational analysis computations then cis-trans or > substituted cyclohexanes. > Almost all elec. packages with HF/DFT or semiempirical or MM contain intro > (manual) about conf analysis. Just give it try to find the part of interest. > > Have a very nice day (or night) all of you. > zoran > > ----- Original Message ----- > > From: "Gonzalo Jim nez-Os s gjimenez/aunizar.es" > To: "Matovic, Zoran D " > Sent: Tuesday, February 09, 2010 9:43 PM > Subject: CCL:G: I have a question for you all > > > > > > Sent to CCL by: "Gonzalo Jim nez-Os s" [gjimenez,unizar.es] > > Dear CCL'ers, > > > > Is it me or the level of the questions submitted to CCL has decreased > > astonishingly in the last few months? I consider myself a young researcher > > and I am still a newbie in some aspects, but the main obligation I impose > > myself before posting a question is to carefully read and search about it > > in > > books, manuals, the web, etc. Of course, this includes software user's > > manuals and lists (I'm tired of deleting messages about Gaussian keywords > > and > > errors). I'm also a newbie professor and I'm experiencing the good and bad > > effects of the "Quick & Easy" concept which is being implanted in our > > students (and in our global society, I'm afraid): "just ask without > > thinking...anyone else will do the job for you. Copy-and-paste will do de > > rest". > > > > The conformational energies of cis/trans-cyclohexane? Seriously, what's > > that > > supossed to mean? Hopely, you mean "substituted cyclohexanes" or > > something...My advice on this: read a basic organic chemistry (at least a > > few > > pages) or ask your teacher/tutor before posting such questions. > > > > By the way, the answer is 'yes'. There are some "special techniques or > > theory > > appliccable", and even "free computational tools under Windows to do this > > work". Moreover, some of us use them (and also their non-free > > counterparts) > > to investigate on real chemical problems and (try to) publish our results. > > It > > has been said that some researchers even obtain public money to support > > their > > research. Can you believe it? > > > > Once the CCL was a reference in computational chemistry and one could read > > directly from the most relevant researchers in the field (unfortunately, > > they > > seem to be out the list these days). This is (intended to be) a serious > > scientific forum and not just the wall of facebook or twitter. > > > > Please, do not make me (and others, for sure) consider incoming CCL > > messages > > as spam. > > > > Peace out, > > > > Gonzalo > > > > PD. Is it really necessary to say "Rocky rocks!" at the end? Just think > > about > > it... > > > > > > > >> From: rocky walden rocky.walden19..gmail.com > > Sent: Tuesday, February 09, 2010 5:58 PM > > To: Oss,GonzaloJimnez > > Subject: CCL: I have a question for you all > > > > > > Hiii People, > > I usually have lot of questions in my mind. The question that worries me > > is > > this thing > > How can we predict the Conformational energies of Cis Trans isomers in > > Cyclohexane using computational tools? > > By the energy values only we are able to tell whether Cis or trans isomer > > is > > stable. > > Let me know if there is any special techniques or theory appliccable. > > Is there any computational tool that does this work (free tool only > > Windows > > Version is preferable). > > > > Cheers > > rocky > > ROCKY !!! ROCKS> > > > -------------------------------------------------------------------------------- > > > > No virus found in this incoming message. > Checked by AVG - www.avg.com > Version: 9.0.733 / Virus Database: 271.1.1/2677 - Release Date: 02/09/10 > 08:35:00> > From owner-chemistry@ccl.net Wed Feb 10 12:51:00 2010 From: "Jamin Krinsky jamink{=}berkeley.edu" To: CCL Subject: CCL: optimaization problem Message-Id: <-41235-100210122438-21930-E2BZrZq/yhCXlBVhgK1zuQ_._server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=001636283e304018dc047f424ef1 Date: Wed, 10 Feb 2010 09:24:24 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink[*]berkeley.edu] --001636283e304018dc047f424ef1 Content-Type: text/plain; charset=ISO-8859-1 Dear Sina, I don't have a huge amount of experience with ONIOM calculations, but I do notice that link atoms are specified in your input, which are normally used for connecting to an MM low layer. You are using DFT on both so you don't need these, although I'm not sure if they have a negative effect or not. Keep in mind that the ONIOM calculation also calculates the entire system at the low level, so using fairly expensive methods for both layers is quite inefficient. If you us a GGA functional (not hybrid) for the opt you can use basis density fitting which might help with speed and possibly convergence, as well as being faster to begin with. Then use that as an initial guess for a hybrid functional calculation. If you send your actual error messages (502 only means something happened in SCF) people might be able to diagnose your problem better. Regards, Jamin On Wed, Feb 10, 2010 at 1:15 AM, sina rastegar sina_rastegar1979(_)yahoo.com wrote: > > Sent to CCL by: "sina rastegar" [sina_rastegar1979|yahoo.com] > I want to optimize a cluster of carbon (c48b12) with calcium which is > dopped in a pentagonal surface.after i want to study the absorption of > hydrogen molecule.I use oniom.this is my route section. > oniom(umpw1pw91/6-31+g(d):ub3lyp/3-21g) > but unfortunately i have the error of link 1502 and when i use scf=qc > the error will be 1508. this is my z-matrix. > B 0 1.59211359 -1.77002419 -2.61421226 L > C 0 2.32007659 -0.42245019 -2.45354626 L H 5 > 0.0000 > C 0 1.61061859 -2.70944519 -1.45756526 L > C 0 0.24659959 -1.45145819 -3.32198626 L > C 0 3.07117559 -0.17752519 -1.27240726 H > C 0 2.36795359 -2.40855519 -0.25303726 L H 11 > 0.0000 > C 0 0.23921059 -0.06605419 -3.61188626 L > C 0 1.45510759 0.61075581 -3.05651726 L > C 0 0.35707459 -3.38759419 -1.08295626 L > C 0 -0.95311842 -2.11455419 -2.88209026 L > C 0 3.03273559 -1.16354019 -0.15060126 H > C 0 1.31415659 1.90652981 -2.51624826 L > B 0 2.89503459 1.19357081 -0.63231126 H > B 0 1.58023459 -3.06929719 0.94888874 L > C 0 0.34942559 -3.74587619 0.30336974 L > C 0 -0.88554542 -3.07249119 -1.79226926 L > B 0 -1.08762142 0.69131181 -3.55927026 L > C 0 -2.27557042 -1.41191619 -2.85137026 L > C 0 3.07970459 -0.44186919 1.15732274 H > C 0 1.49556959 -2.30580519 2.28910775 L > C 0 -2.34964642 -0.05695819 -3.12802226 L > B 0 -3.06258041 -1.99349719 -1.67510526 L > C 0 -2.17984942 -3.06539319 -1.03698526 L > B 0 -0.92235941 -3.58292319 1.08779274 L > C 0 2.97281059 1.01496581 0.88998374 H > C 0 -1.15007042 2.07139680 -2.90723626 L > C 0 0.02237759 2.66967081 -2.48710826 L > C 0 2.04434459 2.25677481 -1.28713826 L H 13 > 0.0000 > B 0 2.31720659 -0.98462819 2.36680774 L H 19 > 0.0000 > C 0 -2.22589442 -3.22579819 0.33373974 L > C 0 -0.96854141 -2.70965219 2.39456174 L > C 0 0.24618259 -2.05174419 2.91341274 L > C 0 1.32005659 3.14493581 -0.44904926 L > B 0 0.00476559 3.54448981 -1.20952226 L > C 0 -3.85729241 -1.04218819 -0.77596526 L > C 0 -3.10186242 0.84924681 -2.21383626 L > C 0 -2.39761542 2.11879781 -2.07600126 L > C 0 2.17568060 1.86072081 1.68211974 L H 25 > 0.0000 > C 0 0.20653659 -0.66109019 3.51366175 L > C 0 1.47574459 0.02273882 3.17063974 L > C 0 1.45101559 1.37821082 2.85665374 L > C 0 1.35240359 2.96153181 1.01284174 L > C 0 -1.29150841 3.70517881 -0.47049726 L > C 0 -2.41078141 2.91488681 -0.86132726 L > C 0 -2.21927141 -2.05727119 2.42885074 L > C 0 -3.01503441 -2.29171719 1.20042374 L > C 0 -3.80804841 -1.24783919 0.69354774 L > C 0 -3.88493741 0.33663681 -1.11721726 L > C 0 -1.01343041 0.00072982 3.61210475 L > B 0 0.13931859 2.19189982 2.92181074 L > C 0 0.19340659 3.23892881 1.76539574 L > B 0 -1.16219841 3.52383981 1.07494874 L > B 0 -2.29952441 -0.69073419 3.11476474 L > C 0 -3.15269041 2.41003081 0.33865474 L > B 0 -3.94326541 1.13349280 0.19951774 L > C 0 -3.88514441 0.09581181 1.34548774 L > C 0 -1.15190841 1.42928382 3.27225774 L > C 0 -2.42292541 2.66860381 1.52103474 L > C 0 -3.17128441 0.40585881 2.48846774 L > C 0 -2.39444841 1.67239182 2.57674874 L > Ca 0 5.27556659 0.06675381 0.06250874 H > H 0 7.27497981 0.09419747 0.02258868 H > H 0 7.87497981 0.09419747 0.02258868 H> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink%berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --001636283e304018dc047f424ef1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sina,
I don't have a huge amount of experience with ONIOM calcu= lations, but I do notice that link atoms are specified in your input, which= are normally used for connecting to an MM low layer. You are using DFT on = both so you don't need these, although I'm not sure if they have a = negative effect or not. Keep in mind that the ONIOM calculation also calcul= ates the entire system at the low level, so using fairly expensive methods = for both layers is quite inefficient. If you us a GGA functional (not hybri= d) for the opt you can use basis density fitting which might help with spee= d and possibly convergence, as well as being faster to begin with. Then use= that as an initial guess for a hybrid functional calculation. If you send = your actual error messages (502 only means something happened in SCF) peopl= e might be able to diagnose your problem better.
Regards,
Jamin

On Wed, Feb 10, 2010 at= 1:15 AM, sina rastegar sina_rastegar1979(_)ya= hoo.com <owner-chemistry%ccl.net> wrote:

Sent to CCL by: "sina =A0rastegar" [sina_rastegar1979|yahoo.com]
I want to optimize a cluster of carbon (c48b12) with calcium which is doppe= d in a pentagonal surface.after i want to study the absorption of hydrogen = molecule.I use oniom.this is my route section.
oniom(umpw1pw91/6-31+g(d):ub3lyp/3-21g)
but unfortunately i have the error of link 1502 and when i use scf=3Dqc
the error will be 1508. this is my z-matrix.
B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.59211359 =A0 -1.77002419 =A0 -2= .61421226 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.32007659 =A0 -0.42245019 =A0= -2.45354626 L H 5 =A0 0.0000
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.61061859 =A0 -2.70944519 =A0= -1.45756526 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.24659959 =A0 -1.45145819 =A0= -3.32198626 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A03.07117559 =A0 -0.17752519 =A0= -1.27240726 H
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.36795359 =A0 -2.40855519 =A0= -0.25303726 L H 11 =A0 0.0000
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.23921059 =A0 -0.06605419 =A0= -3.61188626 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.45510759 =A0 =A00.61075581 = =A0 -3.05651726 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.35707459 =A0 -3.38759419 =A0= -1.08295626 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -0.95311842 =A0 -2.11455419 =A0 -= 2.88209026 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A03.03273559 =A0 -1.16354019 =A0= -0.15060126 H
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.31415659 =A0 =A01.90652981 = =A0 -2.51624826 L
=A0B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.89503459 =A0 =A01.19357081 = =A0 -0.63231126 H
=A0B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.58023459 =A0 -3.06929719 =A0= =A00.94888874 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.34942559 =A0 -3.74587619 =A0= =A00.30336974 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -0.88554542 =A0 -3.07249119 =A0 -= 1.79226926 L
=A0B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -1.08762142 =A0 =A00.69131181 =A0= -3.55927026 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.27557042 =A0 -1.41191619 =A0 -= 2.85137026 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A03.07970459 =A0 -0.44186919 =A0= =A01.15732274 H
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.49556959 =A0 -2.30580519 =A0= =A02.28910775 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.34964642 =A0 -0.05695819 =A0 -= 3.12802226 L
=A0B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -3.06258041 =A0 -1.99349719 =A0 -= 1.67510526 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.17984942 =A0 -3.06539319 =A0 -= 1.03698526 L
=A0B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -0.92235941 =A0 -3.58292319 =A0 = =A01.08779274 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.97281059 =A0 =A01.01496581 = =A0 =A00.88998374 H
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -1.15007042 =A0 =A02.07139680 =A0= -2.90723626 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.02237759 =A0 =A02.66967081 = =A0 -2.48710826 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.04434459 =A0 =A02.25677481 = =A0 -1.28713826 L H 13 =A0 0.0000
=A0B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.31720659 =A0 -0.98462819 =A0= =A02.36680774 L H 19 =A0 0.0000
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.22589442 =A0 -3.22579819 =A0 = =A00.33373974 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -0.96854141 =A0 -2.70965219 =A0 = =A02.39456174 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.24618259 =A0 -2.05174419 =A0= =A02.91341274 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.32005659 =A0 =A03.14493581 = =A0 -0.44904926 L
=A0B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.00476559 =A0 =A03.54448981 = =A0 -1.20952226 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -3.85729241 =A0 -1.04218819 =A0 -= 0.77596526 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -3.10186242 =A0 =A00.84924681 =A0= -2.21383626 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.39761542 =A0 =A02.11879781 =A0= -2.07600126 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A02.17568060 =A0 =A01.86072081 = =A0 =A01.68211974 L H 25 =A0 0.0000
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.20653659 =A0 -0.66109019 =A0= =A03.51366175 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.47574459 =A0 =A00.02273882 = =A0 =A03.17063974 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.45101559 =A0 =A01.37821082 = =A0 =A02.85665374 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A01.35240359 =A0 =A02.96153181 = =A0 =A01.01284174 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -1.29150841 =A0 =A03.70517881 =A0= -0.47049726 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.41078141 =A0 =A02.91488681 =A0= -0.86132726 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.21927141 =A0 -2.05727119 =A0 = =A02.42885074 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -3.01503441 =A0 -2.29171719 =A0 = =A01.20042374 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -3.80804841 =A0 -1.24783919 =A0 = =A00.69354774 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -3.88493741 =A0 =A00.33663681 =A0= -1.11721726 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -1.01343041 =A0 =A00.00072982 =A0= =A03.61210475 L
=A0B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.13931859 =A0 =A02.19189982 = =A0 =A02.92181074 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A00.19340659 =A0 =A03.23892881 = =A0 =A01.76539574 L
=A0B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -1.16219841 =A0 =A03.52383981 =A0= =A01.07494874 L
=A0B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.29952441 =A0 -0.69073419 =A0 = =A03.11476474 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -3.15269041 =A0 =A02.41003081 =A0= =A00.33865474 L
=A0B =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -3.94326541 =A0 =A01.13349280 =A0= =A00.19951774 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -3.88514441 =A0 =A00.09581181 =A0= =A01.34548774 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -1.15190841 =A0 =A01.42928382 =A0= =A03.27225774 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.42292541 =A0 =A02.66860381 =A0= =A01.52103474 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -3.17128441 =A0 =A00.40585881 =A0= =A02.48846774 L
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 -2.39444841 =A0 =A01.67239182 =A0= =A02.57674874 L
=A0Ca =A0 =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 =A05.27556659 =A0 =A00.06675381 =A0= =A00.06250874 H
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A07.27497981 =A0 =A00.09419747 = =A0 =A00.02258868 H
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00 =A0 =A07.87497981 =A0 =A00.09419747 = =A0 =A00.02258868 H



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--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink%berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--001636283e304018dc047f424ef1-- From owner-chemistry@ccl.net Wed Feb 10 15:49:00 2010 From: "zoran matovic zmatovic.,+,.kg.ac.rs" To: CCL Subject: CCL:G: I have a question for you all Message-Id: <-41236-100210153551-26290-o80D67vVBtiLxWnyey+vTg,+,server.ccl.net> X-Original-From: "zoran matovic" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0081_01CAAA98.FA7E42D0" Date: Wed, 10 Feb 2010 21:35:34 +0100 MIME-Version: 1.0 Sent to CCL by: "zoran matovic" [zmatovic ~ kg.ac.rs] This is a multi-part message in MIME format. ------=_NextPart_000_0081_01CAAA98.FA7E42D0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL members: You know what? Reading againg Rocky's realy silly question, I think that Rocky is just = a high school student who has somehow enter into ccl forum to find e.g. = an answer on may be homework requested by his teacher or to impress his = supervisor but knowing a bit of comp chemistry. We judged his e-mail and = he became, I think, a bit scared of such a disscussion not recognizing = the subject. That is may be reason why he has not responded or even = thank to at least three people who gave direct answer.=20 If I am wrong Rocky please correct me.=20 If I am right, dear Rocky do not give up of this matter as it is realy = theoretical chemistry favorite child. So watch this forum, start = learning comp chem, be free to ask (well without "hiii" and "rocky = rocks" if possible) and You'll see that miracles happened and you may = even start to like the chemistry. Now, strongly supporting Gonzalo and Igor complains, my message to all = CCL subscribers: PLEASE READ THE MANUAL OF YOUR QM/SEQM/MM/OR WHATEVER PROGRAMM CAREFULLY = AND DO ALL THE TUTORIAL EXAMPLES BEFORE PLACE YOUR QUESTION TO CCL FORUM With my best regards zoran ----- Original Message -----=20 > From: "Igor Filippov igor.v.filippova/gmail.com" = To: "Matovic, Zoran D " Sent: Wednesday, February 10, 2010 6:25 AM Subject: CCL:G: I have a question for you all >=20 > Sent to CCL by: Igor Filippov [igor.v.filippov-*-gmail.com] > I have to say I agree with Gonzalo on this point. > While everyone is welcome to ask questions, beginning the request with > "Hiii People", and signing it with "ROCKY!!! ROCKS" seems to me (and I > could be in the minority on that) a sign of disrespect, pure and = simple. >=20 > If one is requesting assistance of busy professionals a little = courtesy > can go a long way. I am always happy to help everyone with the = problems > with software I've developed or familiar with, but there are a few > simple things that I implicitly expect from the person asking a > question: > 1) Please be polite. We are not being paid to answer (or even read) = your > questions. > 2) Please sign your email. It does not have to be a real name, but > seeing signature such as "ROCKY!!! ROCKS" or "Blue Power" or some = other > freshman-style nickname makes me feel disrespected. > 3) Please do at least a minimum of research (google search? wikipedia? > anything...) before posting a question. If you cannot be bothered to > type a few words in google why should anyone bother to reply to you? >=20 > Now, this is just my ideas, nobody has to follow or even care about > them. > On the other hand I read Mr. ROCKY!!! ROCKS question only after seeing > the messages from Gonzalo and Zoran, otherwise it would not even > register on my radar with the greeting such as "Hiii People". > I am only writing this because I'm unfortunately seeing more messages > such as this and it saddens me if this is beginning to be accepted as > the norm. >=20 > Just my two cents, > Igor >=20 >=20 > On Tue, 2010-02-09 at 18:54 -0500, zoran matovic zmatovic : kg.ac.rs > wrote: >> Sent to CCL by: "zoran matovic" [zmatovic*_*kg.ac.rs] >> Hello CCL's users, >>=20 >> I have red Gonzalo's reply to "rocky" and (as before to similar = debate) have=20 >> a moderate attitude. May be Rocky has something else on his mind = putting=20 >> quest like this, may be he is young may be senior researcher may be=20 >> unexperienced but has the right to ask for answer. His quest might be = >> considered by computational chemists as silly one, wasting of e-mail = space,=20 >> a quest of one who did not read none of chemistry or comp chem = literature or=20 >> manuals or web pages, but he has the right to ask (this is free forum = for=20 >> everyone) and we may answer to or not to answer. >>=20 >> Well, as far as we consider calcs of cis and trans conformational = energies=20 >> of substituted cyclohexanes there are plenty of literature and web = pages (as=20 >> Gonzalo said) and only what Rocky has to do is to: google or find = wikipedia=20 >> for the next words: conformational analysis computations then = cis-trans or=20 >> substituted cyclohexanes. >> Almost all elec. packages with HF/DFT or semiempirical or MM contain = intro=20 >> (manual) about conf analysis. Just give it try to find the part of = interest. >>=20 >> Have a very nice day (or night) all of you. >> zoran >>=20 >> ----- Original Message -----=20 >> > From: "Gonzalo Jim nez-Os s gjimenez/aunizar.es" = >> To: "Matovic, Zoran D " >> Sent: Tuesday, February 09, 2010 9:43 PM >> Subject: CCL:G: I have a question for you all >>=20 >>=20 >> > >> > Sent to CCL by: "Gonzalo Jim nez-Os s" [gjimenez,unizar.es] >> > Dear CCL'ers, >> > >> > Is it me or the level of the questions submitted to CCL has = decreased >> > astonishingly in the last few months? I consider myself a young = researcher >> > and I am still a newbie in some aspects, but the main obligation I = impose >> > myself before posting a question is to carefully read and search = about it=20 >> > in >> > books, manuals, the web, etc. Of course, this includes software = user's >> > manuals and lists (I'm tired of deleting messages about Gaussian = keywords=20 >> > and >> > errors). I'm also a newbie professor and I'm experiencing the good = and bad >> > effects of the "Quick & Easy" concept which is being implanted in = our >> > students (and in our global society, I'm afraid): "just ask without >> > thinking...anyone else will do the job for you. Copy-and-paste will = do de >> > rest". >> > >> > The conformational energies of cis/trans-cyclohexane? Seriously, = what's=20 >> > that >> > supossed to mean? Hopely, you mean "substituted cyclohexanes" or >> > something...My advice on this: read a basic organic chemistry (at = least a=20 >> > few >> > pages) or ask your teacher/tutor before posting such questions. >> > >> > By the way, the answer is 'yes'. There are some "special techniques = or=20 >> > theory >> > appliccable", and even "free computational tools under Windows to = do this >> > work". Moreover, some of us use them (and also their non-free=20 >> > counterparts) >> > to investigate on real chemical problems and (try to) publish our = results.=20 >> > It >> > has been said that some researchers even obtain public money to = support=20 >> > their >> > research. Can you believe it? >> > >> > Once the CCL was a reference in computational chemistry and one = could read >> > directly from the most relevant researchers in the field = (unfortunately,=20 >> > they >> > seem to be out the list these days). This is (intended to be) a = serious >> > scientific forum and not just the wall of facebook or twitter. >> > >> > Please, do not make me (and others, for sure) consider incoming CCL = >> > messages >> > as spam. >> > >> > Peace out, >> > >> > Gonzalo >> > >> > PD. Is it really necessary to say "Rocky rocks!" at the end? Just = think=20 >> > about >> > it... >> > >> > >> > >> >> From: rocky walden rocky.walden19..gmail.com >> > Sent: Tuesday, February 09, 2010 5:58 PM >> > To: Oss,GonzaloJimnez >> > Subject: CCL: I have a question for you all >> > >> > >> > Hiii People, >> > I usually have lot of questions in my mind. The question that = worries me=20 >> > is >> > this thing >> > How can we predict the Conformational energies of Cis Trans isomers = in >> > Cyclohexane using computational tools? >> > By the energy values only we are able to tell whether Cis or trans = isomer=20 >> > is >> > stable. >> > Let me know if there is any special techniques or theory = appliccable. >> > Is there any computational tool that does this work (free tool only = >> > Windows >> > Version is preferable). >> > >> > Cheers >> > rocky >> > ROCKY !!! ROCKS> >>=20 >>=20 >> = -------------------------------------------------------------------------= ------- >>=20 >>=20 >>=20 >> No virus found in this incoming message. >> Checked by AVG - www.avg.com >> Version: 9.0.733 / Virus Database: 271.1.1/2677 - Release Date: = 02/09/10=20 >> 08:35:00>=20 >> >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20> -------------------------------------------------------------------------= ------- No virus found in this incoming message. Checked by AVG - www.avg.com=20 Version: 9.0.733 / Virus Database: 271.1.1/2679 - Release Date: 02/10/10 = 08:40:00 ------=_NextPart_000_0081_01CAAA98.FA7E42D0 Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCL members:
You know what?
Reading againg Rocky's realy silly = question, I=20 think that Rocky is just a high school student who has somehow enter = into ccl=20 forum to find e.g. an answer on may be homework requested by = his=20 teacher or to impress his supervisor but knowing a bit of = comp=20 chemistry. We judged his e-mail and he became, I think, a bit scared=20 of such a disscussion not recognizing the subject. That = is may be=20 reason why he has not responded or even thank to at least = three people=20 who gave direct answer.
If I am wrong Rocky please correct = me.=20
If I am right, dear Rocky do not give = up of this=20 matter as it is realy theoretical chemistry favorite child. = So watch=20 this forum, start learning comp chem, be free to ask (well without = "hiii"=20 and "rocky rocks" if possible) and You'll see that miracles = happened=20 and you may even start to like the chemistry.
 
Now, strongly supporting Gonzalo = and Igor=20 complains, my message to all CCL subscribers:
 
PLEASE READ THE MANUAL OF YOUR=20 QM/SEQM/MM/OR WHATEVER PROGRAMM CAREFULLY AND DO ALL THE = TUTORIAL=20 EXAMPLES BEFORE PLACE YOUR QUESTION TO CCL FORUM
 
 
With my best regards
zoran
 
 
----- Original Message -----
To: "Matovic, Zoran D " = <zmatovic++kg.ac.yu>
Sent: Wednesday, February 10, 2010 6:25 = AM
Subject: CCL:G: I have a question for = you=20 all

>
> Sent to CCL by: Igor Filippov=20 [igor.v.filippov-*-gmail.com]
> I have to say I agree with Gonzalo = on this=20 point.
> While everyone is welcome to ask questions, beginning the = request=20 with
> "Hiii People", and signing it with "ROCKY!!! ROCKS" seems = to me=20 (and I
> could be in the minority on that) a sign of disrespect, = pure and=20 simple.
>
> If one is requesting assistance of busy = professionals a=20 little courtesy
> can go a long way. I am always happy to help = everyone=20 with the problems
> with software I've developed or familiar with, = but=20 there are a few
> simple things that I implicitly expect from the = person=20 asking a
> question:
> 1) Please be polite. We are not being = paid to=20 answer (or even read) your
> questions.
> 2) Please sign = your email.=20 It does not have to be a real name, but
> seeing signature such as = "ROCKY!!! ROCKS" or "Blue Power" or some other
> freshman-style = nickname=20 makes me feel disrespected.
> 3) Please do at least a minimum of = research=20 (google search? wikipedia?
> anything...) before posting a = question. If=20 you cannot be bothered to
> type a few words in google why should = anyone=20 bother to reply to you?
>
> Now, this is just my ideas, = nobody has=20 to follow or even care about
> them.
> On the other hand I = read Mr.=20 ROCKY!!! ROCKS question only after seeing
> the messages from = Gonzalo and=20 Zoran, otherwise it would not even
> register on my radar with the = greeting such as "Hiii People".
> I am only writing this because = I'm=20 unfortunately seeing more messages
> such as this and it saddens = me if=20 this is beginning to be accepted as
> the norm.
>
> = Just my=20 two cents,
> Igor
>
>
> On Tue, 2010-02-09 at = 18:54=20 -0500, zoran matovic zmatovic : kg.ac.rs
> wrote:
>> Sent = to CCL=20 by: "zoran matovic" [zmatovic*_*kg.ac.rs]
>> Hello CCL's=20 users,
>>
>> I have red Gonzalo's reply to "rocky" = and (as=20 before to similar debate) have
>> a moderate attitude. May be = Rocky=20 has something else on his mind putting
>> quest like this, may = be he=20 is young may be senior researcher may be
>> unexperienced but = has the=20 right to ask for answer. His quest might be
>> considered by=20 computational chemists as silly one, wasting of e-mail space, =
>> a=20 quest of one who did not read none of chemistry or comp chem literature = or=20
>> manuals or web pages, but he has the right to ask (this is = free=20 forum for
>> everyone) and we may answer to or not to=20 answer.
>>
>> Well, as far as we consider calcs of = cis and=20 trans conformational energies
>> of substituted cyclohexanes = there are=20 plenty of literature and web pages (as
>> Gonzalo said) and = only what=20 Rocky has to do is to: google or find wikipedia
>> for the = next words:=20 conformational analysis computations then cis-trans or
>> = substituted=20 cyclohexanes.
>> Almost all elec. packages with HF/DFT or = semiempirical=20 or MM contain intro
>> (manual) about conf analysis. Just give = it try=20 to find the part of interest.
>>
>> Have a very nice = day (or=20 night) all of you.
>> zoran
>>
>> ----- = Original=20 Message -----
>> > From: "Gonzalo Jim nez-Os s = gjimenez/aunizar.es"=20 <owner-chemistry|,|ccl.net>
>> To: "Matovic, Zoran D "=20 <zmatovic|,|kg.ac.yu>
>> Sent: Tuesday, February 09, 2010 = 9:43=20 PM
>> Subject: CCL:G: I have a question for you all
>> =
>>
>> >
>> > Sent to CCL by: = "Gonzalo =20 Jim  nez-Os  s" [gjimenez,unizar.es]
>> > Dear=20 CCL'ers,
>> >
>> > Is it me or the level of the=20 questions submitted to CCL has decreased
>> > astonishingly = in the=20 last few months? I consider myself a young researcher
>> > = and I am=20 still a newbie in some aspects, but the main obligation I = impose
>>=20 > myself before posting a question is to carefully read and search = about it=20
>> > in
>> > books, manuals, the web, etc. Of = course,=20 this includes software user's
>> > manuals and lists (I'm = tired of=20 deleting messages about Gaussian keywords
>> > = and
>> >=20 errors). I'm also a newbie professor and I'm experiencing the good and=20 bad
>> > effects of the "Quick & Easy" concept which is = being=20 implanted in our
>> > students (and in our global society, = I'm=20 afraid): "just ask without
>> > thinking...anyone else will = do the=20 job for you. Copy-and-paste will do de
>> > = rest".
>>=20 >
>> > The conformational energies of = cis/trans-cyclohexane?=20 Seriously, what's
>> > that
>> > supossed to = mean?=20 Hopely, you mean "substituted cyclohexanes" or
>> > = something...My=20 advice on this: read a basic organic chemistry (at least a
>> = >=20 few
>> > pages) or ask your teacher/tutor before posting = such=20 questions.
>> >
>> > By the way, the answer is = 'yes'.=20 There are some "special techniques or
>> > = theory
>> >=20 appliccable", and even "free computational tools under Windows to do=20 this
>> > work". Moreover, some of us use them (and also = their=20 non-free
>> > counterparts)
>> > to investigate = on real=20 chemical problems and (try to) publish our results.
>> >=20 It
>> > has been said that some researchers even obtain = public money=20 to support
>> > their
>> > research. Can you = believe=20 it?
>> >
>> > Once the CCL was a reference in=20 computational chemistry and one could read
>> > directly = > from the=20 most relevant researchers in the field (unfortunately,
>> > = they
>> > seem to be out the list these days). This is = (intended to=20 be) a serious
>> > scientific forum and not just the wall of = facebook or twitter.
>> >
>> > Please, do not = make me=20 (and others, for sure) consider incoming CCL
>> >=20 messages
>> > as spam.
>> >
>> > = Peace=20 out,
>> >
>> > Gonzalo
>> = >
>> >=20 PD. Is it really necessary to say "Rocky rocks!" at the end? Just think=20
>> > about
>> > it...
>> = >
>>=20 >
>> >
>> >> From: rocky walden=20 rocky.walden19..gmail.com
>> > Sent: Tuesday, February 09, = 2010 5:58=20 PM
>> > To: Oss,GonzaloJimnez
>> > Subject: CCL: = I have=20 a question for you all
>> >
>> >
>> = > Hiii=20 People,
>> >  I usually have lot of questions in my = mind. The=20 question that worries me
>> > is
>> > this=20 thing
>> > How can we predict the Conformational energies of = Cis=20 Trans isomers in
>> > Cyclohexane using computational=20 tools?
>> > By the energy values only we are able to tell = whether=20 Cis or trans isomer
>> > is
>> > = stable.
>>=20 > Let me know if there is any special techniques or theory=20 appliccable.
>> > Is there any computational tool that does = this=20 work (free tool only
>> > Windows
>> > Version = is=20 preferable).
>> >
>> > Cheers
>> >=20 rocky
>> > ROCKY !!! ROCKS>
>>
>> =
>>=20 -------------------------------------------------------------------------= -------
>>=20
>>
>>
>> No virus found in this incoming=20 message.
>> Checked by AVG - www.avg.com
>>=20 Version: 9.0.733 / Virus Database: 271.1.1/2677 - Release Date: 02/09/10 =
>> 08:35:00>
>>
>
>
> =
> -=3D=20 This is automatically added to each message by the mailing script = =3D-
> To=20 recover the email address of the author of the message, please = change
>=20 the strange characters on the top line to the ++ sign. You can = also
> look=20 up the X-Original-From: line in the mail header.
>
> E-mail = to=20 subscribers: CHEMISTRY++ccl.net or = use:
>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>
> E-mail to administrators: CHEMISTRY-REQUEST++ccl.net or=20 use
>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>
> Subscribe/Unsubscribe:=20
>      http://www.ccl.net/chemistry/sub_unsub.shtml
<= FONT=20 size=3D2 face=3DArial>>
> Before posting, check wait time at: = http://www.ccl.net
>=20
> Job: http://www.ccl.net/jobs
>=20 Conferences: http://server.ccl.net/chemistry/announcements/conferences/
>
> Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
>
> If your mail bounces from CCL with = 5.7.1 error,=20 check:
>      http://www.ccl.net/spammers.txt
>
> RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
>


No virus found in this incoming=20 message.
Checked by AVG - www.avg.com =
Version: 9.0.733 /=20 Virus Database: 271.1.1/2679 - Release Date: 02/10/10=20 08:40:00
 ------=_NextPart_000_0081_01CAAA98.FA7E42D0-- From owner-chemistry@ccl.net Wed Feb 10 17:07:00 2010 From: "Reynier Suard az reynier.suardiaz:-:gmail.com" To: CCL Subject: CCL: Summary of "software to list chi1 angles" Message-Id: <-41237-100210165820-26911-vdCRLacrEkMdB1pH0lgUHw : server.ccl.net> X-Original-From: "Reynier Suard az" Date: Wed, 10 Feb 2010 16:58:17 -0500 Sent to CCL by: "Reynier Suard az" [reynier.suardiaz:gmail.com] I would like to thanks people who respond to my question. Here is a summary of the suggested softwares: -software to list chi1 angles- Vadar http://redpoll.pharmacy.ualberta.ca/vadar/ Dang http://kinemage.biochem.duke.edu/software/dang.php Chimera http://www.cgl.ucsf.edu/chimera/index.html icm-browser http://www.molsoft.com/icm_browser.html with best regards reynier -- _______________________________________________________ Dr. Reynier Suardaz e-mail: reynier#fq.uh.cu Dpto.de Qumica Fsica telf.: +53 7 8780684 Facultad de Qumica La Habana, 10400 Universidad de La Habana Cuba url: http://www.fq.uh.cu/investig/gqf/e/lrsdr_en.html _______________________________________________________ From owner-chemistry@ccl.net Wed Feb 10 23:46:01 2010 From: "Lev Gorenstein lev|a|ledorub.poxod.com" To: CCL Subject: CCL: Summary of "software to list chi1 angles" Message-Id: <-41238-100210192021-1868-tZy5oQnUiPuFIxSF0Biq8A%server.ccl.net> X-Original-From: Lev Gorenstein Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 10 Feb 2010 18:49:00 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Lev Gorenstein [lev() ledorub.poxod.com] On Wed, 10 Feb 2010, Reynier Suard az reynier.suardiaz:-:gmail.com wrote: RSar> I would like to thanks people who respond to my question. Here RSar> is a summary of the suggested softwares: RSar> RSar> -software to list chi1 angles- RSar> RSar> Vadar RSar> http://redpoll.pharmacy.ualberta.ca/vadar/ RSar> Dang RSar> http://kinemage.biochem.duke.edu/software/dang.php RSar> Chimera RSar> http://www.cgl.ucsf.edu/chimera/index.html RSar> icm-browser RSar> http://www.molsoft.com/icm_browser.html And if you are command line/scripting inclined, a 'dihed.pl' script > from the MMTSB toolset can list any dihedrals. See http://blue11.bch.msu.edu/mmtsb/Main_Page - About toolset http://blue11.bch.msu.edu/mmtsb/dihed.pl - About the dihed.pl BTW, 'analyzeCHARMM.pl' script from the toolset can do the same (and a lot more!) for not just a single structure, but for a whole MD trajectory. Regards, Lev -- "DOS computers manufactured by companies such as IBM, Compaq, Tandy, and millions of others are by far the most popular, with about 70 million machines in use worldwide. Macintosh fans, on the other hand, may note that cockroaches are far more numerous than humans, and that numbers alone do not denote a higher life form." -- New York Times, November 26, 1991.