From owner-chemistry@ccl.net Thu Jul 5 03:31:00 2007 From: "Oleksandr Oleksandras nablaoblada+*+yahoo.com" To: CCL Subject: CCL:G: limited integer representation in Gaussian, bad length for file Message-Id: <-34653-070705032802-8559-9I4OrvW01sFjQY0hFNRuaQ+/-server.ccl.net> X-Original-From: "Oleksandr Oleksandras" Date: Thu, 5 Jul 2007 03:27:59 -0400 Sent to CCL by: "Oleksandr Oleksandras" [nablaoblada**yahoo.com] Changing Maxdisk option does not have any effect. The disc space is not the problem, since I used series of 250MW rwf files, which have been only half-filled during calculation. But increasing dynamic memory "%mem" (limit is 2GB) gives the decrease in "Estimate disk for full transformation -677255533 words" on exactly the same amount. Obviously, a negative number for required diskspace is nonsense. Any other ideas? --- "Alexander Isaeyv alex]~[ccmsi.us" wrote: > > Sent to CCL by: "Alexander Isaeyv" [alex~!~ccmsi.us] > Oleksandr, > > It looks like there is not enough disk space. > Try to increase it with MaxDisk keyword. > http://www.gaussian.com/g_ur/k_maxdisk.htm > However, depending on your hardware and/or gaussian > version you might be limited to 2gb per file. In > this case you can split rwf file using the following > keyword: > %RWF=loc1,size1,loc2,size2, ... > > Hope this will help, > Alexandr > > ------------------------------------------------------- > > Alexandr Isayev, > Graduate Research Assistant, and System > Administrator > * Computational Center for Molecular Structure > and Interactions (CCMSI), > Jackson State University, > Jackson, MS USA > Tel: +(601) 979-1134 > e-mail: alex(at)ccmsi.us > Web: http://www.ccmsi.us > -------------------------------------------------------- > > > ---------- Original Message > ---------------------------------- > > From: "Oleksandr Oleksandras > nablaoblada*yahoo.com" > Reply-To: "CCL Subscribers" > Date: Wed, 4 Jul 2007 08:11:00 -0400 > > > > >Sent to CCL by: "Oleksandr Oleksandras" > [nablaoblada:yahoo.com] > >Hi > >Does anybody know how to overcome the following > error in Gaussian > >"Estimate disk for full transformation -677255533 > words. Semi-Direct transformation. > >Bad length for file." > >Thank you > >Oleksandr> > > > > > > > > From owner-chemistry@ccl.net Thu Jul 5 04:35:00 2007 From: "Oleksandr nablaoblada : yahoo.com" To: CCL Subject: CCL:G: limited integer representation in Gaussian, bad length for file. Message-Id: <-34654-070705042237-4974-D01zSfnM0pHk4dq0iERBgw||server.ccl.net> X-Original-From: Oleksandr Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 5 Jul 2007 00:22:27 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Oleksandr [nablaoblada- -yahoo.com] Changing Maxdisk option does not have any effect. The disc space is not the problem, since I used series of 250MW rwf files, which have been only half-filled during calculation. But increasing dynamic memory "%mem" (limit is 2GB) gives the decrease in "Estimate disk for full transformation -677255533 words" on exactly the same amount. Obviously, a negative number for required diskspace is nonsense. Any other ideas? --- "Alexander Isaeyv alex]~[ccmsi.us" wrote: > > Sent to CCL by: "Alexander Isaeyv" [alex~!~ccmsi.us] > Oleksandr, > > It looks like there is not enough disk space. > Try to increase it with MaxDisk keyword. > http://www.gaussian.com/g_ur/k_maxdisk.htm > However, depending on your hardware and/or gaussian > version you might be limited to 2gb per file. In > this case you can split rwf file using the following > keyword: > %RWF=loc1,size1,loc2,size2, ... > > Hope this will help, > Alexandr > > ------------------------------------------------------- > > Alexandr Isayev, > Graduate Research Assistant, and System > Administrator > * Computational Center for Molecular Structure > and Interactions (CCMSI), > Jackson State University, > Jackson, MS USA > Tel: +(601) 979-1134 > e-mail: alex(at)ccmsi.us > Web: http://www.ccmsi.us > -------------------------------------------------------- > > > ---------- Original Message > ---------------------------------- > > From: "Oleksandr Oleksandras > nablaoblada*yahoo.com" > Reply-To: "CCL Subscribers" > Date: Wed, 4 Jul 2007 08:11:00 -0400 > > > > >Sent to CCL by: "Oleksandr Oleksandras" > [nablaoblada:yahoo.com] > >Hi > >Does anybody know how to overcome the following > error in Gaussian > >"Estimate disk for full transformation -677255533 > words. Semi-Direct transformation. > >Bad length for file." > >Thank you > >Oleksandr> > > > > > > > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the * > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST * ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > ____________________________________________________________________________________ Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL From owner-chemistry@ccl.net Thu Jul 5 05:44:01 2007 From: "Maxim Kholin maxim.kholin[*]q-pharm.com" To: CCL Subject: CCL: molecular modeling for pharmacy students Message-Id: <-34655-070704022817-10911-TNwH5DBcrmT+xZQwPCkzlw/a\server.ccl.net> X-Original-From: "Maxim Kholin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="koi8-r"; reply-type=original Date: Wed, 4 Jul 2007 10:29:50 +0400 MIME-Version: 1.0 Sent to CCL by: "Maxim Kholin" [maxim.kholin[-]q-pharm.com] Hello, Arthur Quantum Pharmaceuticals offers customised drug design exercises for universities and colleges. Please go to www.q-pharm.com to learn more about Quantum computer aided drug design technology. Maxim ----- Original Message ----- > From: "Arthur G. Cox acox/asouthuniversity.edu" To: "Kholin, Maxim N " Sent: Wednesday, July 04, 2007 12:21 AM Subject: CCL: molecular modeling for pharmacy students > > Sent to CCL by: "Arthur G. Cox" [acox%x%southuniversity.edu] > I am trying to formulate a 3 hour computer laboratory exercise to > illustrate the use of computers in drug design for pharmacy students. Can > anyone point me towards recources or software that could be useful in this > regard? > > Thanks -Art Cox> > > From owner-chemistry@ccl.net Thu Jul 5 05:45:01 2007 From: "Lukasz Cwiklik cwiklik[-]gmail.com" To: CCL Subject: CCL: Managing downloaded reference pdf files Message-Id: <-34656-070705051756-29732-Q1QY/E7gpHW5oeWuhqNlKw^^^server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 5 Jul 2007 11:17:24 +0200 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik*gmail.com] Hi, This is a little bit out of the topic but you can organize your bibliography data using a new online service created by Nature Publishing Group: http://www.connotea.org It has no possibility to manage local pdf files but can deal with a new papers found on-line. And if you want just to easily index and search pdfs on your local machine you can use Google Desktop - ok, this is a somehow evil, whatever the company claims, but my scientific colleagues are using it ;) Best, Lukasz Cwiklik -- Lukasz Cwiklik http://cwiklik.wordpress.com > >> -----Original Message----- > >> From: owner-chemistry * ccl.net [mailto:owner-chemistry * ccl.net] > >> Sent: 02 July 2007 14:27 > >> To: Sherwood, P (Paul) > >> Subject: CCL: Managing downloaded reference pdf files > >> > >> > >> > >> Sent to CCL by: "Bhabani S Mallik" [mbhabani_+_yahoo.com] > >> Dear All, > >> > >> I want to manage all my reference pdf files ( huge number) > >> with a proper way. > >> I mean is there any software which can convert all my files > >> to browsable > >> html pages with title, author, year of publication and a > >> link to that pdf file ? > >> > >> From owner-chemistry@ccl.net Thu Jul 5 06:24:00 2007 From: "Dominic Ryan dominic.ryan . comcast.net" To: CCL Subject: CCL: molecular modeling for pharmacy students Message-Id: <-34657-070704232442-14684-VDZzTojmaUSjWlO/7lle6A ~~ server.ccl.net> X-Original-From: Dominic Ryan Content-Type: multipart/alternative; boundary="------------050803080204040309060705" Date: Wed, 04 Jul 2007 22:51:55 -0400 MIME-Version: 1.0 Sent to CCL by: Dominic Ryan [dominic.ryan-#-comcast.net] This is a multi-part message in MIME format. --------------050803080204040309060705 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit I have had some experience teaching molecular modeling at various levels. Pharmacy students will lack most of what one would regard as a base for understanding the impact of molecular modeling using many of the details we all sweat over. I recommend a focus on aspects of molecular recognition: shape and molecular properties. Molecular properties could include conformational energies, but I think that opens up too big a topic for the purpose at hand. Getting across that a protein's binding site(s) have a distinct shape with distinct requirements for matching up properties gets to the heart of the drug design / recognition problem of perhaps greatest interest to pharmacy students. To assemble a computational lab I would worry less about the specifics of a given set of programs and more about the real lesson you are trying to communicate. I think that no matter what you chose as a vehicle the onus will fall to the author of the lab to construct a lesson and that this construction will require more effort than you would think it should. Having said that, you might find that MOE from chemcomp.com offers some useful advantages, but they are certainly not the only game in town. They do offer some very useful breadth of capabilities for what you are describing. One could be tempted to organize it into protein and small molecule blocks, but I suggest a structure first around concepts and secondarily around molecular size: Structural variability: Proteins: structural errors or ambiguities Proteins: motion and partial relevance of a crystal structure. Small molecules: conformational sampling Small molecules: Structural ambiguities Molecular properties Non polar interactions Polar interactions and the cost of desolvation Perhaps this reflects my own bias, but I believe that grounding in experimental uncertainties allows a person to put a value on computational methods. Such a structure above would allow large expansion of any area or keeping it fairly contained within a 3-4 hour block but still get across the broad strokes of what we are grappling with. This could include what one might do when imporant data is missing structurally and how it may be worth trying to construct an in silico model of behaviour (QSAR). The heart of it has to be how computational methods can derive useful information from the data at hand -be it historical or current. Dominic Ryan DRI Consulting Phil Hultin hultin[-]cc.umanitoba.ca wrote: > Sent to CCL by: "Phil Hultin" [hultin**cc.umanitoba.ca] > I did a series of 4 3-hour workshops on molecular modeling (as distinct from > quantum mechanical calculations) for 4th-year honours chemistry and > biochemistry students this year. My experience suggested to me that perhaps > you are being over-optimistic if you want to do something meaningful with > "computers in drug design" in just a single 3 hour session. > > You face several challenges, some of which I suspect will be more severe > with Pharmacy students than they were with Chemistry students - but even > Chemistry students struggled with some ideas that just don't get much > coverage in typical undergraduate curricula. > > 1) The concept of a potential energy surface. Seems kind of obvious when > you've been using computational methods for a while but it is surprising how > this idea gets mixed up in students' minds. > 2) Energy minimization methods - a "minimization" is not an automatic method > of finding "the best geometry" but that is how many undergraduate students > perceive it. I found several times that students would arrive at bizarre > structures but would not question the result because "I did a minimization!" > 3) Understanding the results - I found that students tended to focus on one > thing only: the "final energy". In a group of almost 20 students, about 3/4 > of them never even drew the structure corresponding to the minimum energy. > When asked to discuss why this structure was lower in energy than an > alternative structure that came from the modeling, most of them did not look > at the specific interactions that we had discussed and that were the > building blocks for the force fields we had used (another concept they had > trouble with). > > I won't even get into the issues of dealing with multiple minima and > ensemble averages, but suffice to say that at least in our undergraduate > program the students never do quantitative conformational analysis of > systems much more complicated than n-butane. Suddenly they are being asked > to carry out a computational exploration of a drug/receptor complex and they > just don't have all the conceptual tools to understand what is going on. > > Finally, you come to actually using the programs available. Yes, the > typical undergraduate is "more computer literate" than was the case even 5 > years ago, but what does that actually mean? The students today know how to > download music from iTunes, and how to read their Hotmail, and how to sign > on to Facebook, but the majority of them know nothing at all about how to > actually run a computer. So, now you want them to run a molecular modeling > program. If you have a budget you can buy several licenses of a program > like Hyperchem which is fairly easy to use from the students' point of view > (although perhaps not the professional choice for computational research), > but if you have to rely on freeware you have a problem. > 1) UNIX or LINUX-based programs that are used by most researchers are out of > the question for most undergraduates. It would take several hours just to > get them to understand how to start up a text editor, write an input file, > use it to start a job, then open the output file and find the results. It > gets worse if the program requires that you build topology files etc before > submitting the actual calculation (eg. Gromacs). > 2) Windows-based freeware like ArgusLab or Tinker appear to be good choices > but I have found that they don't work on all computers. If you have a > dedicated computer lab you can install the programs and figure out whether > they are compatible in advance, but it is surprising how many problems can > arise from differences in the hardware from one computer to the next. I > thoroughly validated some exercises on ArgusLab and Tinker with my own > computer, only to find that the programs crashed for unexplained reasons on > other machines, while they worked on another subset of hardware. (Please, > let's not get into Mac vs. Windows here - the reality is that we are > probably talking about Windows machines). > > I encourage you to do something with modeling in your class, but in 3 hours > you will barely be able to give them the conceptual foundation to understand > how to search for and identify the energetically relevant minima (in the gas > phase) for the drug by itself. I don't think it is very useful just to give > them a set of step-by-step instructions for a program and get them to push > the buttons without understanding what they are doing. > > Dr. Philip G. Hultin > > Professor of Chemistry, > > University of Manitoba > > Winnipeg, MB > > R3T 2N2 > > hultin%a%cc.umanitoba.ca > > http://umanitoba.ca/chemistry/people/hultin > > > -----Original Message----- > >> From: owner-chemistry%a%ccl.net [mailto:owner-chemistry%a%ccl.net] >> > Sent: July 3, 2007 3:22 PM > To: Hultin, Philip G. > Subject: CCL: molecular modeling for pharmacy students > > > Sent to CCL by: "Arthur G. Cox" [acox%x%southuniversity.edu] > I am trying to formulate a 3 hour computer laboratory exercise to illustrate > the use of computers in drug design for pharmacy students. Can anyone point > me towards recources or software that could be useful in this regard? > > Thanks -Art Coxhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > > > --------------050803080204040309060705 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit I have had some experience teaching molecular modeling at various levels. Pharmacy students will lack most of what one would regard as a base for understanding the impact of molecular modeling using many of the details we all sweat over.

I recommend a focus on aspects of molecular recognition: shape and molecular properties.

Molecular properties could include conformational energies, but I think that opens up too big a topic for the purpose at hand. Getting across that a protein's binding site(s) have a distinct shape with distinct requirements for matching up properties gets to the heart of the drug design / recognition problem of perhaps greatest interest to pharmacy students.

To assemble a computational lab I would worry less about the specifics of a given set of programs and more about the real lesson you are trying to communicate. I think that no matter what you chose as a vehicle the onus will fall to the author of the lab to construct a lesson and that this construction will require more effort than you would think it should. Having said that, you might find that MOE from chemcomp.com offers some useful advantages, but they are certainly not the only game in town. They do offer some very useful breadth of capabilities for what you are describing.

One could be tempted to organize it into protein and small molecule blocks, but I suggest a structure first around concepts and secondarily around molecular size:
Structural variability:
    Proteins: structural errors or ambiguities
    Proteins: motion and partial relevance of a crystal structure.
    Small molecules: conformational sampling
    Small molecules: Structural ambiguities
Molecular properties
    Non polar interactions
    Polar interactions and the cost of desolvation

Perhaps this reflects my own bias, but I believe that grounding in experimental uncertainties allows a person to put a value on computational methods.

Such a structure above would allow large expansion of any area or keeping it fairly contained within a 3-4 hour block but still get across the broad strokes of what we are grappling with. This could include what one might do when imporant data is missing structurally and how it may be worth trying to construct an in silico model of behaviour (QSAR). The heart of it has to be how computational methods can derive useful information from the data at hand -be it historical or current.

Dominic Ryan
DRI Consulting

Phil Hultin hultin[-]cc.umanitoba.ca wrote:

Sent to CCL by: "Phil Hultin" [hultin**cc.umanitoba.ca]
I did a series of 4 3-hour workshops on molecular modeling (as distinct from
quantum mechanical calculations) for 4th-year honours chemistry and
biochemistry students this year.  My experience suggested to me that perhaps
you are being over-optimistic if you want to do something meaningful with
"computers in drug design" in just a single 3 hour session.

You face several challenges, some of which I suspect will be more severe
with Pharmacy students than they were with Chemistry students - but even
Chemistry students struggled with some ideas that just don't get much
coverage in typical undergraduate curricula.

1) The concept of a potential energy surface.  Seems kind of obvious when
you've been using computational methods for a while but it is surprising how
this idea gets mixed up in students' minds.
2) Energy minimization methods - a "minimization" is not an automatic method
of finding "the best geometry" but that is how many undergraduate students
perceive it.  I found several times that students would arrive at bizarre
structures but would not question the result because "I did a minimization!"
3) Understanding the results - I found that students tended to focus on one
thing only: the "final energy".  In a group of almost 20 students, about 3/4
of them never even drew the structure corresponding to the minimum energy.
When asked to discuss why this structure was lower in energy than an
alternative structure that came from the modeling, most of them did not look
at the specific interactions that we had discussed and that were the
building blocks for the force fields we had used (another concept they had
trouble with).

I won't even get into the issues of dealing with multiple minima and
ensemble averages, but suffice to say that at least in our undergraduate
program the students never do quantitative conformational analysis of
systems much more complicated than n-butane.  Suddenly they are being asked
to carry out a computational exploration of a drug/receptor complex and they
just don't have all the conceptual tools to understand what is going on.

Finally, you come to actually using the programs available.  Yes, the
typical undergraduate is "more computer literate" than was the case even 5
years ago, but what does that actually mean?  The students today know how to
download music from iTunes, and how to read their Hotmail, and how to sign
on to Facebook, but the majority of them know nothing at all about how to
actually run a computer.  So, now you want them to run a molecular modeling
program.  If you have a budget you can buy several licenses of a program
like Hyperchem which is fairly easy to use from the students' point of view
(although perhaps not the professional choice for computational research),
but if you have to rely on freeware you have a problem.
1) UNIX or LINUX-based programs that are used by most researchers are out of
the question for most undergraduates.  It would take several hours just to
get them to understand how to start up a text editor, write an input file,
use it to start a job, then open the output file and find the results.  It
gets worse if the program requires that you build topology files etc before
submitting the actual calculation (eg. Gromacs).
2) Windows-based freeware like ArgusLab or Tinker appear to be good choices
but I have found that they don't work on all computers.  If you have a
dedicated computer lab you can install the programs and figure out whether
they are compatible in advance, but it is surprising how many problems can
arise from differences in the hardware from one computer to the next.  I
thoroughly validated some exercises on ArgusLab and Tinker with my own
computer, only to find that the programs crashed for unexplained reasons on
other machines, while they worked on another subset of hardware.  (Please,
let's not get into Mac vs. Windows here - the reality is that we are
probably talking about Windows machines).

I encourage you to do something with modeling in your class, but in 3 hours
you will barely be able to give them the conceptual foundation to understand
how to search for and identify the energetically relevant minima (in the gas
phase) for the drug by itself.  I don't think it is very useful just to give
them a set of step-by-step instructions for a program and get them to push
the buttons without understanding what they are doing.

Dr. Philip G. Hultin

Professor of Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

hultin%a%cc.umanitoba.ca

http://umanitoba.ca/chemistry/people/hultin


-----Original Message-----

From: owner-chemistry%a%ccl.net [mailto:owner-chemistry%a%ccl.net]

Sent: July 3, 2007 3:22 PM
To: Hultin, Philip G. 
Subject: CCL: molecular modeling for pharmacy students

Sent to CCL by: "Arthur G. Cox" [acox%x%southuniversity.edu]
I am trying to formulate a 3 hour computer laboratory exercise to illustrate
the use of computers in drug design for pharmacy students. Can anyone point
me towards recources or software that could be useful in this regard? 

Thanks -Art Coxhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtE-mail to subscribers: CHEMISTRY_._ccl.net or use:
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Hello,

The autonom feature = of ISIS draw can generate names for individual molecules. I am not sure whethe= r it will work for a database.

HTH

Regards

Mohamed Diwan

University of Kentuc= ky

From:= owner-chemistry[]ccl.net [mailto:owner-chemistry[]ccl.net]
Sent: Thursday, July 05, 200= 7 11:04 AM
To: Abdul Hameed, MohamedDiw= anMo
Subject: CCL: Converting structures to IUPAC names

Dear Colleagues,

Does anyone know an application which is capable to convert structures to IUPAC names of a larger database?

Best regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-860= 0 - D=FCbendorf - Switzerland
T:+41-44-824 2164 - F:+41-44-8242926 - http:= //www.givaudan.com

--_000_62D3F106CB16C34D825A1B75EFBA6839D5869104EX7FM04adukyedu_-- From owner-chemistry@ccl.net Thu Jul 5 15:25:01 2007 From: "Greg Warren greg^^^eyesopen.com" To: CCL Subject: CCL: Converting structures to IUPAC names Message-Id: <-34669-070705132350-23088-bCIx+G3ltLy1bhp6NBoEIA]*[server.ccl.net> X-Original-From: Greg Warren Content-Type: multipart/alternative; boundary="------------030104030601090709070601" Date: Thu, 05 Jul 2007 10:52:08 -0600 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg(-)eyesopen.com] This is a multi-part message in MIME format. --------------030104030601090709070601 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit One among several options is Lexichem (structure to IUPAC name) and its complement Ogham (name to structure) from OpenEye Scientific Software. http://www.eyesopen.com http://www.eyesopen.com/products/toolkits/lexichem.html http://www.eyesopen.com/products/toolkits/ogham.html andras.borosy/./givaudan.com wrote: > > Dear Colleagues, > > Does anyone know an application which is capable to convert structures > to IUPAC names of a larger database? > > Best regards, > > Dr. Andr�s P�ter Borosy > Scientific Modelling Expert > Fragrance Research > Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D�bendorf > - Switzerland > T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com -- ======================================== Gregory Warren, PhD OpenEye Scientific Software, Inc 9 Bisbee Court, Suite D Santa Fe, NM 87508 (505) 473-7385 ext 50 mailto:greg]![eyesopen.com ======================================== --------------030104030601090709070601 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit One among several options is Lexichem (structure to IUPAC name) and its complement Ogham (name to structure) from OpenEye Scientific Software.

http://www.eyesopen.com
http://www.eyesopen.com/products/toolkits/lexichem.html
http://www.eyesopen.com/products/toolkits/ogham.html

andras.borosy/./givaudan.com wrote:

Dear Colleagues,

Does anyone know an application which is capable to convert structures to IUPAC names of a larger database?

Best regards,

Dr. András Péter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf - Switzerland
T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com

-- 
========================================
Gregory Warren, PhD
OpenEye Scientific Software, Inc
9 Bisbee Court, Suite D
Santa Fe, NM 87508
(505) 473-7385 ext 50
mailto:greg]![eyesopen.com
========================================

--------------030104030601090709070601-- From owner-chemistry@ccl.net Thu Jul 5 16:00:00 2007 From: "Karen.Green!^!sanofi-aventis.com" To: CCL Subject: CCL: Beilstein's Autonom RE: Converting structures to IUPAC names Message-Id: <-34670-070705125541-31467-lo3r82maKJwdAR7cCbdPJg,server.ccl.net> X-Original-From: content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7BF20.B25F7D43" Date: Thu, 5 Jul 2007 09:22:35 -0700 MIME-Version: 1.0 Sent to CCL by: [Karen.Green*sanofi-aventis.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C7BF20.B25F7D43 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I think Beilstein's Autonom will do that for you. See: http://www.mdl.com/products/framework/autonom/key_features.jsp =20 Karen=20 --- Karen M. Green, Ph.D. Karen.Green|a|sanofi-aventis.com Research Investigator Sanofi Aventis Pharmaceuticals =20 _____ =20 > From: owner-chemistry|a|ccl.net [mailto:owner-chemistry|a|ccl.net]=20 Sent: Thursday, July 05, 2007 8:04 AM To: Green, Karen M. PH/US Subject: CCL: Converting structures to IUPAC names Dear Colleagues,=20 Does anyone know an application which is capable to convert structures = to IUPAC names of a larger database?=20 Best regards,=20 Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf = - Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com ------_=_NextPart_001_01C7BF20.B25F7D43 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

I think Beilstein's Autonom will do that for=20 you.

See: h= ttp://www.mdl.com/products/framework/autonom/key_features.jsp<= /SPAN>

Karen

---

Karen M. Green,=20 Ph.D.

Karen.Green|a|sanofi-aventis= .com

Research=20 Investigator

Sanofi Aventis=20 Pharmaceuticals

From: owner-chemistry|a|ccl.net=20 [mailto:owner-chemistry|a|ccl.net]
Sent: Thursday, July 05, = 2007 8:04=20 AM
To: Green, Karen M. PH/US
Subject: CCL: = Converting=20 structures to IUPAC names

Dear Colleagues,=20

Does anyone know an application = which is=20 capable to convert structures to IUPAC names of a larger = database?=20

Best regards, =

Dr. Andr=E1s P=E9ter Borosy
Scientific = Modelling=20 Expert
Fragrance Research
Givaudan Schweiz AG -=20 Ueberlandstrasse 138 - CH-8600 - = D=FCbendorf -=20 Switzerland
T:+41-44-824 2164 - F:+41-44-8242926 = =20 - http://www.givaudan.com ------_=_NextPart_001_01C7BF20.B25F7D43-- From owner-chemistry@ccl.net Thu Jul 5 18:49:01 2007 From: "Wayne Steinmetz WES04747+*+pomona.edu" To: CCL Subject: CCL: molecular modeling for pharmacy students Message-Id: <-34671-070705163413-1243-x993cI0q6ynu9BmTbzCDEg..server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 5 Jul 2007 12:56:57 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747%x%pomona.edu] If the students have no experience with molecular modeling, one 3-hour session is not enough. Students at Pomona have an introduction to modeling in General Chemistry. They encounter more examples in organic chemistry. Therefore, the students who take my modeling course are able to move on to more interesting cases. You may be interested in the lab exercises that I have developed. Go to my index page provided below. The link for Chemistry 51 will direct you to our modeling experiment for freshmen. The link for the modeling course will contain all the handouts and the exercises. Software? We use Spartan. There is a very inexpensive student version that has most of the tools. The product has an excellent GUI and is virtually bug free. For more advanced techniques, I use SYBYL. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz],[pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.net] Sent: Wednesday, July 04, 2007 7:38 AM To: Wayne Steinmetz Subject: CCL: molecular modeling for pharmacy students Sent to CCL by: "Phil Hultin" [hultin**cc.umanitoba.ca] I did a series of 4 3-hour workshops on molecular modeling (as distinct > from quantum mechanical calculations) for 4th-year honours chemistry and biochemistry students this year. My experience suggested to me that perhaps you are being over-optimistic if you want to do something meaningful with "computers in drug design" in just a single 3 hour session. You face several challenges, some of which I suspect will be more severe with Pharmacy students than they were with Chemistry students - but even Chemistry students struggled with some ideas that just don't get much coverage in typical undergraduate curricula. 1) The concept of a potential energy surface. Seems kind of obvious when you've been using computational methods for a while but it is surprising how this idea gets mixed up in students' minds. 2) Energy minimization methods - a "minimization" is not an automatic method of finding "the best geometry" but that is how many undergraduate students perceive it. I found several times that students would arrive at bizarre structures but would not question the result because "I did a minimization!" 3) Understanding the results - I found that students tended to focus on one thing only: the "final energy". In a group of almost 20 students, about 3/4 of them never even drew the structure corresponding to the minimum energy. When asked to discuss why this structure was lower in energy than an alternative structure that came from the modeling, most of them did not look at the specific interactions that we had discussed and that were the building blocks for the force fields we had used (another concept they had trouble with). I won't even get into the issues of dealing with multiple minima and ensemble averages, but suffice to say that at least in our undergraduate program the students never do quantitative conformational analysis of systems much more complicated than n-butane. Suddenly they are being asked to carry out a computational exploration of a drug/receptor complex and they just don't have all the conceptual tools to understand what is going on. Finally, you come to actually using the programs available. Yes, the typical undergraduate is "more computer literate" than was the case even 5 years ago, but what does that actually mean? The students today know how to download music from iTunes, and how to read their Hotmail, and how to sign on to Facebook, but the majority of them know nothing at all about how to actually run a computer. So, now you want them to run a molecular modeling program. If you have a budget you can buy several licenses of a program like Hyperchem which is fairly easy to use from the students' point of view (although perhaps not the professional choice for computational research), but if you have to rely on freeware you have a problem. 1) UNIX or LINUX-based programs that are used by most researchers are out of the question for most undergraduates. It would take several hours just to get them to understand how to start up a text editor, write an input file, use it to start a job, then open the output file and find the results. It gets worse if the program requires that you build topology files etc before submitting the actual calculation (eg. Gromacs). 2) Windows-based freeware like ArgusLab or Tinker appear to be good choices but I have found that they don't work on all computers. If you have a dedicated computer lab you can install the programs and figure out whether they are compatible in advance, but it is surprising how many problems can arise from differences in the hardware from one computer to the next. I thoroughly validated some exercises on ArgusLab and Tinker with my own computer, only to find that the programs crashed for unexplained reasons on other machines, while they worked on another subset of hardware. (Please, let's not get into Mac vs. Windows here - the reality is that we are probably talking about Windows machines). I encourage you to do something with modeling in your class, but in 3 hours you will barely be able to give them the conceptual foundation to understand how to search for and identify the energetically relevant minima (in the gas phase) for the drug by itself. I don't think it is very useful just to give them a set of step-by-step instructions for a program and get them to push the buttons without understanding what they are doing. Dr. Philip G. Hultin Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin%a%cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin -----Original Message----- > From: owner-chemistry%a%ccl.net [mailto:owner-chemistry%a%ccl.net] Sent: July 3, 2007 3:22 PM To: Hultin, Philip G. Subject: CCL: molecular modeling for pharmacy students Sent to CCL by: "Arthur G. Cox" [acox%x%southuniversity.edu] I am trying to formulate a 3 hour computer laboratory exercise to illustrate the use of computers in drug design for pharmacy students. Can anyone point me towards recources or software that could be useful in this regard? Thanks -Art Coxhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/che mistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. From owner-chemistry@ccl.net Thu Jul 5 19:25:00 2007 From: "Yann Tambouret yannpaul/./chem.bu.edu" To: CCL Subject: CCL: Gaussian, restart, modify geom, new optimization: help Message-Id: <-34672-070705155047-31923-6cwTnnXz5SpwvuxTkRdOXA*|*server.ccl.net> X-Original-From: Yann Tambouret Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 05 Jul 2007 15:19:15 -0400 MIME-Version: 1.0 Sent to CCL by: Yann Tambouret [yannpaul]^[chem.bu.edu] I'm trying to optimize a structure, using a z-matrix that has all variables and no constants. Like so: %chk=CHECKFILE %mem=200MW %nproc=1 #P rhf/3-21g nosymm OPT Title here 0 1 <> Variables: <> This works fine. Now I want to use the produced checkpoint file as a starting off point for a partial optimization, were I read in the structure, adjust some variables, and freeze them. I thought I should use OPT and GEOM=MODIFY, and add a new section at the bottom of the input. Like so: %chk=CHECKFILE %mem=200MW %nproc=1 #P rhf/3-21g nosymm OPT geom=MODIFY Some title here 0 1 hx -1.00 F I've been getting the following error: H,0,7.0608945649,-0.0001132533,6.5960156671 H,0,8.2517504997,0.0001356526,2.5119212904 H,0,8.8433295344,0.0000189394,4.9011600351 Recover connectivity data from disk. The following ModRedundant input section has been read: Invalid extra data found. hx -0.100 F This method does work if hx was originally frozen, but that's not what I'm looking for. I want a full optimization, followed by freezing some variables (to something other then their optimized value) and optimizing the rest. Any suggestions on how to do this? -Yann From owner-chemistry@ccl.net Thu Jul 5 23:55:01 2007 From: "Sue Lam chsue2004#,#yahoo.com" To: CCL Subject: CCL:G: Problems with oscillator strengths in TDDFT Message-Id: <-34673-070705235230-24100-npaEEgkIzIjXbLvJfIMzTQ*server.ccl.net> X-Original-From: Sue Lam Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1517323829-1183693943=:8969" Date: Thu, 5 Jul 2007 20:52:23 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004**yahoo.com] --0-1517323829-1183693943=:8969 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi. Is the calculated oscillator strengths for those two singlet transitions the same, if you break down the symmetry of the [Ru(bpy)3]2+ molecule? Best regards, Sue "Arvydas Tamulis tamulis_._mserv.itpa.lt" wrote: Sent to CCL by: Arvydas Tamulis [tamulis.:.mserv.itpa.lt] Dear Colleagues, We have calculated spectrum and oscillator strengths of D3 symmetry complex [Ru(bpy)3]2+ using TDDFT B3LYP with the LanL2DZ basis set and IEFPCM or COSMO water solvent shell models in Gaussian03 or ORCA program packages. We have received two singlet-E lines: 456.18 nm (0.0140 oscillator strength) and 435.61 nm (0.1373 oscillator strength). Experiment of [Ru(bpy)3]2+ derivatives gives two peaks: one at about 450 nm (intensity 1.0 arbitrary units) and the other near 430 nm (intensity 0.6 arbitrary units) therefore the values of our calculated intensities are reversible in comparison with experiment. Oscillator strength calculations done by G03 and ORCA are exactly the same wrong calculating with PBEPBE potential using 6-311G* basis set. My impression is that it is something wrong in B3LYP, PBEPBE potentials when calculating oscillator strengths by Gaussian03 and ORCA programs of the D3 symmetry complexes and their derivatives while the values of spectral lines are exactly good. It is interesting that even ZINDO gives the right intensities in comparison with experiment but the values of spectral lines are shifted strongly. Maybe you can advise some good program with DFT potential/basis set for the calculations of right oscillator strengths of the D3 symmetry complexes and their derivatives? In the case if you are far from the field of calculations of oscillator strengths in G03 or ORCA, would you please to forward my question to developers of program packages who are working on subroutine of calculations of oscillator strengths in G03, ORCA or people who possesses the good subroutine. For regular organic compounds the oscillator strengths obtained by TDDFT in G03 and ORCA are good. More about our research you can see in our website www.itpa.lt/~tamulis/ and press on button For PACE project WEBsite With best regards, Arvydas Tamulishttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. --0-1517323829-1183693943=:8969 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Hi. Is the calculated oscillator strengths for those two singlet transitions the same, if you break down the symmetry of the [Ru(bpy)3]2+ molecule?

Best regards,

Sue

"Arvydas Tamulis tamulis_._mserv.itpa.lt" <owner-chemistry|a|ccl.net> wrote:

Sent to CCL by: Arvydas Tamulis [tamulis.:.mserv.itpa.lt]

Dear Colleagues,

We have calculated spectrum and oscillator strengths of D3 symmetry
complex [Ru(bpy)3]2+ using TDDFT B3LYP with the LanL2DZ
basis set and IEFPCM or COSMO water solvent shell models in
Gaussian03 or ORCA program packages. We have received two
singlet-E lines: 456.18 nm (0.0140 oscillator strength) and
435.61 nm (0.1373 oscillator strength).
Experiment of [Ru(bpy)3]2+ derivatives gives two peaks:
one at about 450 nm (intensity 1.0 arbitrary units) and the
other near 430 nm (intensity 0.6 arbitrary units)
therefore the values of our calculated intensities are reversible in
comparison with experiment.
Oscillator strength calculations done by G03 and
ORCA are exactly the same wrong calculating with PBEPBE potential
using 6-311G* basis set.
My impression is that it is something wrong in B3LYP, PBEPBE potentials
when calculating oscillator strengths by Gaussian03 and ORCA programs
of the D3 symmetry complexes and their derivatives
while the values of spectral lines are exactly good.
It is interesting that even ZINDO gives the right intensities in
comparison with experiment but the values of spectral lines are
shifted strongly. Maybe you can advise some good program with DFT
potential/basis set for the calculations of right oscillator strengths of
the D3 symmetry complexes and their derivatives?

In the case if you are far from the field of calculations of oscillator
strengths in G03 or ORCA, would you please to forward my question to
developers of program packages who are working on subroutine
of calculations of oscillator strengths in G03, ORCA or people who
possesses the good subroutine.

For regular organic compounds the oscillator strengths obtained by
TDDFT in G03 and ORCA are good.
More about our research you can see in our website
www.itpa.lt/~tamulis/ and press on button
For PACE project WEBsite

With best regards,
Arvydas Tamulis

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