From owner-chemistry@ccl.net Mon Aug 11 00:00:00 2008 From: "Ralf Tonner ralf.tonner^^googlemail.com" To: CCL Subject: CCL:G: Inaccurate quadrature in CalDSu Message-Id: <-37538-080810193725-24104-LnR0S+3HH49EQBSgbQGOUg^server.ccl.net> X-Original-From: Ralf Tonner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 11 Aug 2008 10:40:52 +1200 MIME-Version: 1.0 Sent to CCL by: Ralf Tonner [ralf.tonner^googlemail.com] Hi Teobald, it sounds like your integration grid for the DFT calculation is not fine-grained enough. If you receive this error message in the first few SCF steps you can use > scf(NoVarAcc) This prevents G03 from using looser integral-accuracy for the first SCF steps. If the integrals are still not accurate enough you could try > integral(ultrafine) For consistency reasons you should apply the same integral accuracy to all calculations of a batch. Hope this helps Ralf. -- Dr. Ralf Tonner Centre of Theoretical Chemistry and Physics New Zealand Institute for Advanced Study Massey University Auckland NEW ZEALAND Phone (64) 09 414 0800 extn 9894 Fax (64) 09 443 9779 ---- Teobald Kupka teobaldk^yahoo.com schrieb: > Sent to CCL by: "Teobald Kupka" [teobaldk]=[yahoo.com] > Hi, > > I am trying to calculate indirect spin-spin coupling constants in G03 using DFT and unc-ccJ-pVXZ basis sets. Job fails with a message: > > Inaccurate quadrature in CalDSu > > The job is OK for RHF calculations with the same basis set or with DFT/ccJ-pVXZ . I have tried suggested on this list guess=INDO without luck. > > I would appreciate any suggestions. > > Teobald Kupka > Unioversity of Opole, > Opole > teobaldk-$-yahoo.com> > > From owner-chemistry@ccl.net Mon Aug 11 03:00:00 2008 From: "mudit dixit dixitmuditk]|[gmail.com" To: CCL Subject: CCL: Hydrogen Storage Message-Id: <-37539-080811022004-32191-BQ/xCAGGsAXh5EV8/Ilonw!^!server.ccl.net> X-Original-From: "mudit dixit" Date: Mon, 11 Aug 2008 02:20:01 -0400 Sent to CCL by: "mudit dixit" [dixitmuditk..gmail.com] > "Mr Shabbir shabbir * nenu.edu.cn" wrote: > > Sent to CCL by: "Mr Shabbir" [shabbir=nenu.edu.cn] > > > > "Mudit k Dixit dixitmuditk^^gmail.com" wrote: > > > > Sent to CCL by: "Mudit k Dixit" [dixitmuditk * gmail.com] > > what are the pakages I can use to study Hydrogen storage materials. > > thanks > > mudit > > > > Hi, > Orca is a new software that can specially take weak interactions into account.It is free of cost.u can find on google..It will help u for this type of interactions > Regards > Mr.Shabbir > > THank you very much, for help. Mudit From owner-chemistry@ccl.net Mon Aug 11 04:22:00 2008 From: "laxmikanth rao lkjoshiji**yahoo.com" To: CCL Subject: CCL: error opening file Message-Id: <-37540-080811033047-16984-w1Mf3llePDy3lQovPh2Q+A^^server.ccl.net> X-Original-From: laxmikanth rao Content-Type: multipart/alternative; boundary="0-147391548-1218436230=:40181" Date: Mon, 11 Aug 2008 12:00:30 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: laxmikanth rao [lkjoshiji~~yahoo.com] --0-147391548-1218436230=:40181 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Naser=0ABefore starting job, you have to start the log file with some = name and then select the method in " setup" and then got to "compute".=0AI = hope you got the point. If you have problems feel free to contact.=0Awith w= arm regrds=0ADr. J.Laxmikanth Rao=0AComputational Chemistry=0AInorganic Che= mistry=0AIICT, HYderabad-500 007, A.P. INDIA=0A=0A=0A----- Original Message= ----=0AFrom: naser eltaher eltayeb nasertaha90a/yahoo.co.uk =0ATo: "Rao, J.laxmikanth " =0ASent= : Monday, 11 August, 2008 5:41:36 AM=0ASubject: CCL: error opening file=0A= =0A=0ASent to CCL by: "naser eltaher eltayeb" [nasertaha90]|[yahoo.co.uk]= =0ADear All=0A=0AI am trying to do some calculations on zindo/1 in Hyperche= m, using file .pdb , I start the log file , after a few mints of calculatio= n I get this message "error in opening file .log", could anyone help me to = solve this problem.=0A=0AThank you=0ANaser E. Eltayeb=0A=0A=0A=0A-=3D This = is automatically added to each message by the mailing script =3D-=0ATo reco= ver the email address of the author of the message, please change=0Athe str= ange characters on the top line to the ]|[ sign. You can also=0Alook up the X= -Original-From: line in the mail header.=0A=0AE-mail to subscribers: CHEMIS= TRY]|[ccl.net or use:=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST]|[ccl.net or= use=0A=C2=A0 =C2=A0 =C2=A0= =0A=0A=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/che= mistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: http://www.= ccl.net=0A=0A=0AConferences: http://server.ccl= .net/chemistry/announcements/conferences/=0A=0ASearch Messages: http://www.= ccl.net/htdig=C2=A0 (login: ccl, Password: search)=0A=0AIf your mail bounce= s from CCL with 5.7.1 error, check:=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.n= et/spammers.txt=0A=0ARTFI: http://www.ccl.net/chemistry/aboutccl/instructio= ns/=0A=0A=0A Unlimited freedom, unlimited storage. Get it now, on http= ://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/ --0-147391548-1218436230=:40181 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear Naser
=0A
 
=0A
Before starting job= , you have to start the log file with some name and then select the method = in " setup" and then got to "compute".
=0A
 
=0A
I h= ope you got the point. If you have problems feel free to contact.
=0A<= DIV> 
=0A
with warm regrds
=0A
 
=0A
D= r. J.Laxmikanth Rao
=0A
Computational Chemistry
=0A
Inorg= anic Chemistry
=0A
IICT, HYderabad-500 007, A.P. INDIA
=0A =0A
 
=0A

=0A
----- Original Message ----
= > From: naser eltaher eltayeb nasertaha90a/yahoo.co.uk <owner-chemistry]|[cc= l.net>
To: "Rao, J.laxmikanth " <lkjoshiji]|[yahoo.com>Sent: Monday, 11 August, 2008 5:41:36 AM
Subject: CCL: error opening f= ile


Sent to CCL by: "naser eltaher eltayeb" [nasertaha90]|[yahoo= .co.uk]
Dear All

I am trying to do some calculations on zindo/1 i= n Hyperchem, using file .pdb , I start the log file , after a few mints of = calculation I get this message "error in opening file .log", could anyone h= elp me to solve this problem.

Thank you
Naser E. Eltayeb

<= BR>
-=3D This is automatically added to each message by the mailing scri= pt =3D-
To recover the email address of the author of the message, pleas= e change
the strange characters on the top line to the ]|[ sign. You can a= lso
E-mail to subscribers: CHEMISTRY]|[ccl.net or use= :
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= /A>

E-mail to administrators: CHEMISTRY-REQUEST]|[ccl.n= et or use
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Add more friends to your messenger and enjoy! Invite them now. --0-147391548-1218436230=:40181-- From owner-chemistry@ccl.net Mon Aug 11 10:10:01 2008 From: "Egon Willighagen egon.willighagen,,gmail.com" To: CCL Subject: CCL: Exact definitions of Sybyl atom types? Message-Id: <-37541-080811100836-527-HybR70warnFuzggT78d34w/./server.ccl.net> X-Original-From: "Egon Willighagen" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 11 Aug 2008 15:09:09 +0200 MIME-Version: 1.0 Sent to CCL by: "Egon Willighagen" [egon.willighagen+*+gmail.com] Dear all, does anyone know a good reference for the definition of the 28 original Sybyl atom types [0], as web resources like [1] are typically short on information? For example, I am looking for the scope of the O.co2 and N.am atom types. The former is listed for carboxylate and phosphate groups, but says little about R groups... would [CO3]2- oxygens also be marked as O.co2, and what if the phosphate group is bound, like in ATP, etc, which oxygens would still be O.co2 then? Regarding the N.am, would an 'amide' nitrogen in a ring systems, e.g. as in this ZINC structure [2] still be marked as N.am, or is this restricted to nitrogens as found in peptide bonds? Surely, there are a few lists around which link these types to SMARTS, but would love to find some reference of the original intended meaning of those atom types. Looking forward to hearing from you, kind regards, Egon Willighagen 0.N. Van Openbosch, R. Cramer III, and F.F. Giarrusso, Sybyl, the integrated molecular modelling system. J. Mol. Graph, 1985, 3(3):110-111 1.http://www.tripos.com/mol2/atom_types.html 2.http://zinc.docking.org/srchdb.pl?zinc=ZINC03249299 -- ---- http://chem-bla-ics.blogspot.com/ From owner-chemistry@ccl.net Mon Aug 11 13:56:00 2008 From: "Joseph M Leonard jleonard42+/-gmail.com" To: CCL Subject: CCL: Exact definitions of Sybyl atom types? Message-Id: <-37542-080811134013-12928-eKs0HrPPeKh2L1eJ1ZBKBA^^server.ccl.net> X-Original-From: "Joseph M Leonard" Content-Type: multipart/alternative; boundary="----=_Part_6339_10071207.1218472640769" Date: Mon, 11 Aug 2008 12:37:20 -0400 MIME-Version: 1.0 Sent to CCL by: "Joseph M Leonard" [jleonard42~!~gmail.com] ------=_Part_6339_10071207.1218472640769 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline As I recall, there are SLN-based typing rules files in the SYBYL distribution (or at least they were there years ago)... While not SMARTS patters, it should be straightforward converting one to the other. Look in one of the tables sub-directories, or grep the SYBYL tree for anything containing things like O.co2? Joe Leonard jleonard42_-_gmail.com On Mon, Aug 11, 2008 at 9:09 AM, Egon Willighagen egon.willighagen,, gmail.com wrote: > > Sent to CCL by: "Egon Willighagen" [egon.willighagen+*+gmail.com] > Dear all, > > does anyone know a good reference for the definition of the 28 > original Sybyl atom types [0], as web resources like [1] are typically > short on information? > > For example, I am looking for the scope of the O.co2 and N.am atom > types. The former is listed for carboxylate and phosphate groups, but > says little about R groups... would [CO3]2- oxygens also be marked as > O.co2, and what if the phosphate group is bound, like in ATP, etc, > which oxygens would still be O.co2 then? Regarding the N.am, would an > 'amide' nitrogen in a ring systems, e.g. as in this ZINC structure [2] > still be marked as N.am, or is this restricted to nitrogens as found > in peptide bonds? > > Surely, there are a few lists around which link these types to SMARTS, > but would love to find some reference of the original intended meaning > of those atom types. > > Looking forward to hearing from you, > > kind regards, > > Egon Willighagen > > 0.N. Van Openbosch, R. Cramer III, and F.F. Giarrusso, Sybyl, the > integrated molecular modelling system. J. Mol. Graph, 1985, > 3(3):110-111 > 1.http://www.tripos.com/mol2/atom_types.html > 2.http://zinc.docking.org/srchdb.pl?zinc=ZINC03249299 > > -- > ---- > http://chem-bla-ics.blogspot.com/> > > -- There's no reason to think that primitive hunter gatherers were any happier than we are, and even less reason to imagine we'll be happier if we imitate their management practices. ------=_Part_6339_10071207.1218472640769 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
As I recall, there are SLN-based typing rules files in the SYBYL distribution (or at least they were there years ago)...  While not SMARTS patters, it should be straightforward converting one to the other.  Look in one of the tables sub-directories, or grep the SYBYL tree for anything containing things like O.co2?

Joe Leonard
jleonard42_-_gmail.com

On Mon, Aug 11, 2008 at 9:09 AM, Egon Willighagen egon.willighagen,,gmail.com <owner-chemistry_-_ccl.net> wrote:

Sent to CCL by: "Egon Willighagen" [egon.willighagen+*+gmail.com]
Dear all,

does anyone know a good reference for the definition of the 28
original Sybyl atom types [0], as web resources like [1] are typically
short on information?

For example, I am looking for the scope of the O.co2 and N.am atom
types. The former is listed for carboxylate and phosphate groups, but
says little about R groups... would [CO3]2- oxygens also be marked as
O.co2, and what if the phosphate group is bound, like in ATP, etc,
which oxygens would still be O.co2 then? Regarding the N.am, would an
'amide' nitrogen in a ring systems, e.g. as in this ZINC structure [2]
still be marked as N.am, or is this restricted to nitrogens as found
in peptide bonds?

Surely, there are a few lists around which link these types to SMARTS,
but would love to find some reference of the original intended meaning
of those atom types.

Looking forward to hearing from you,

kind regards,

Egon Willighagen

0.N. Van Openbosch, R. Cramer III, and F.F. Giarrusso, Sybyl, the
integrated molecular modelling system. J. Mol. Graph, 1985,
3(3):110-111
1.http://www.tripos.com/mol2/atom_types.html
2.http://zinc.docking.org/srchdb.pl?zinc=ZINC03249299

--
----
http://chem-bla-ics.blogspot.com/



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--
There's no reason to think that primitive hunter gatherers were any happier than we are, and even less reason to imagine we'll be happier if we imitate their management practices.
------=_Part_6339_10071207.1218472640769-- From owner-chemistry@ccl.net Mon Aug 11 17:42:01 2008 From: "Vincent Leroux vincent.leroux%x%loria.fr" To: CCL Subject: CCL: Exact definitions of Sybyl atom types? Message-Id: <-37543-080811131116-10338-MxPps1ulpfG46D/+2PQnqg[]server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 11 Aug 2008 18:32:47 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux||loria.fr] Hi Egon, For some examples for ambiguous Sybyl atom type definitions, you can see : http://www.ccdc.cam.ac.uk/support/documentation/gold/4_0/gold/gold.1.58.html#245104 Note that different programs may favor different atom type assignments in such cases... To my knowledge O.co2 can be used to designate a partly charged oxygen in a group of equivalent oxygens, so in CO3-- and in phosphate groups like with ATP you can use O.co2 on the terminal oxygens. In such cases the ar bond type may also be used to denote partly double bonds. But in both cases some programs may not be pleased... Regarding the ZINC structure you provided the proposed mol2 file (probably generated by OpenEye routines) uses the N.am type, but some programs might prefer N.ar... If given the choice I would first try the latter as to make sure aromaticity will be detected. Note that for consistency if you have an N.am atom you should have an am bond (which is the case here), if you have N.ar all aromatic bonds should be marked as ar. Best advice I could give you is to experiment on the program you are feeding your structures with and try to spot the cases where there could be mistakes. Read the log files and check that if aromaticity is reported here it is done so correctly for structures such as the ZINC one you provided. Is the program is able to perform corrections when in trouble interpreting atom and bond types, and if so is it efficient? Can the calculation start even after there are errors in that area (some programs discard "unknown" atoms and proceed... others crash immediately)? You can have quick answers by introducing ambiguous and wrong atom types for testing purposes. If the results are not clear then "bad" mol2 input is probably risky. In such a case, if sdf input is accepted, you should favor it, assuming that the program is able to deduce its own correct atom types from the connectivity and protonation state of each molecule. If you start from SMARTS/SMILES you can use Corina to generate 3d sdf or mol2 files in which the atom types are going to fit most cases (but check the protonation)... You probably do not want to code all the conversion work from scratch. Egon Willighagen egon.willighagen,,gmail.com a écrit : > Sent to CCL by: "Egon Willighagen" [egon.willighagen+*+gmail.com] > Dear all, > > does anyone know a good reference for the definition of the 28 > original Sybyl atom types [0], as web resources like [1] are typically > short on information? > > For example, I am looking for the scope of the O.co2 and N.am atom > types. The former is listed for carboxylate and phosphate groups, but > says little about R groups... would [CO3]2- oxygens also be marked as > O.co2, and what if the phosphate group is bound, like in ATP, etc, > which oxygens would still be O.co2 then? Regarding the N.am, would an > 'amide' nitrogen in a ring systems, e.g. as in this ZINC structure [2] > still be marked as N.am, or is this restricted to nitrogens as found > in peptide bonds? > > Surely, there are a few lists around which link these types to SMARTS, > but would love to find some reference of the original intended meaning > of those atom types. > > Looking forward to hearing from you, > > kind regards, > > Egon Willighagen > > 0.N. Van Openbosch, R. Cramer III, and F.F. Giarrusso, Sybyl, the > integrated molecular modelling system. J. Mol. Graph, 1985, > 3(3):110-111 > 1.http://www.tripos.com/mol2/atom_types.html > 2.http://zinc.docking.org/srchdb.pl?zinc=ZINC03249299 > > From owner-chemistry@ccl.net Mon Aug 11 20:58:01 2008 From: "Debasish Banerjee debasishbanerjee2007- -gmail.com" To: CCL Subject: CCL: Ab-initio and DFT sources Message-Id: <-37544-080811132620-11761-++Z+HlkJEc3s0a2doRQVMg/a\server.ccl.net> X-Original-From: "Debasish Banerjee" Date: Mon, 11 Aug 2008 13:26:15 -0400 Sent to CCL by: "Debasish Banerjee" [debasishbanerjee2007*o*gmail.com] Hi I need to learn VASP, Wiek 2K for ab-initio and DFT calculations. Can anybody please suggest some good online links, books, papers, workshops or training for beginners? Thank you, D. Banerjee, PhD