From owner-chemistry@ccl.net Fri Mar 24 04:43:00 2006 From: "Anselm.Horn:+:chemie.uni-erlangen.de" To: CCL Subject: CCL: How to create a b&w contour plot containing a cutout Message-Id: <-31307-060323163421-24819-dttFXCZCQ7JFRv3q5So+OA*_*server.ccl.net> X-Original-From: Anselm.Horn%%chemie.uni-erlangen.de Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 23 Mar 2006 21:37:36 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Anselm.Horn^chemie.uni-erlangen.de Dear all, I'm sorry, if this is a bit off-topic. When looking for a way to visualize the electrostatic potential of planar systems, one very often finds black&white contour plots, one in the plane, one above (e.g. Ford&Wang, J. Comput. Chem. 1993, 14, 1101-1111). Does anybody know a program that could create such graphics from 2D raw data? Of course, I tried gnuplot, but I faced the following problem: The property values in the plane near the atomic cores were omitted in the above paper, and in the contour plot graphic the lewis structure of the molecule is shown there. However, I cannot tell gnuplot to omit the respective data, because it needs a complete set of rows and columns. On the other hand, if one simply sets the values, that are to omit, to a very high or low constant, the countour lines near the molecular border are probably not correctly calculated (or am I wrong?). The same problems arise with xmgrace, unfortunately. Any hints are welcome! Best regards, Anselm Horn Computer-Chemie-Centrum Friedrich-Alexander-Universitaet Erlangen-Nuernberg Germany From owner-chemistry@ccl.net Fri Mar 24 09:04:00 2006 From: "John McKelvey jmmckel%x%attglobal.net" To: CCL Subject: CCL: Wireless cluster Message-Id: <-31308-060324090202-15696-3zyiUpGqofzj6NR5ZYEtEQ(~)server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 24 Mar 2006 08:56:09 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel!^!attglobal.net] Cheers! Please don't laugh, or maybe this is so funny [ridiculous?] that you'll get a good laugh, and it will make your day! Anyway, I want to build a small linux cluster [6-8 total processors] but don't have a lot of cooling in one place. Running wires would not be practical, if not impossible Now, the application is extremely coarse-grain, and only a very, very small amount of data gets moved about once initialization of a job is done.. Can it be done "wireless?" Please share your laughs... Cheers.. John McKelvey From owner-chemistry@ccl.net Fri Mar 24 09:39:01 2006 From: "Elaine Meng meng[A]cgl.ucsf.edu" To: CCL Subject: CCL: Docking to Cyps Message-Id: <-31309-060323125710-28866-2qW9SiyGRcvBitWzy3z18Q__server.ccl.net> X-Original-From: Elaine Meng Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Thu, 23 Mar 2006 09:17:53 -0800 Mime-Version: 1.0 (Apple Message framework v746.3) Sent to CCL by: Elaine Meng [meng(-)cgl.ucsf.edu] Hello, This paper may be of interest (includes docking and experimental results): Verras A, Kuntz ID, Ortiz de Montellano PR. Computer-assisted design of selective imidazole inhibitors for cytochrome p450 enzymes. J Med Chem. 2004 Jul 1;47(14):3572-9. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15214784&query_hl=1&itool =pubmed_docsum On Mar 23, 2006, at 8:14 AM, Axel Mathieu AMathieu++tranzyme.com wrote: > Sent to CCL by: "Axel Mathieu" [AMathieu===tranzyme.com] > > =20 > Greetings again to the community, > Following the recent publication of the human P450c2D6 X-Ray > crystal - > J Biol Chem. 2006 Mar 17;281(11):7614-22, we are considering embarking > on docking studies of our pharmacological candidates to a series of > human P450's to aid us in the design of molecules with enhanced P450 > profiles. PK profiling is very important in drug design, I'm not > teaching anything new here, and several human P450 X-Ray structures > have > been published now. Homology modeling of these has been going on for > years but what I'm interested in are studies with the X-Ray > structures. > =20 > I was thus wondering if some people would like to have a (short) > discussion of the relevance of this docking given the known > flexibility > of these proteins and in some cases, the presence of large labile > active > sites (such as for Cyp3A4). I'm really interested in personal > experience > if you're willing to boast a bit ;o), docking methods used, > validity of > the results, etc, anything that comes to mind. I understand that we > are > in a world of confidential results and I accept if no one is > willing to > share. Simple suggestions and pointers to good papers on this subject > are also quite acceptable and absolute details are not necessary. > =20 > We can definitely take this discussion off the CCL newsgroup, if > desired. > Thanks, > APM > =20 ----- Elaine C. Meng, Ph.D. meng!A!cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Fri Mar 24 10:49:01 2006 From: "Ross Walker ross%%rosswalker.co.uk" To: CCL Subject: CCL: Bandwidth prediction Message-Id: <-31311-060324021927-945-e0bbGLKrn23UXjA0A+gljw(0)server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 23 Mar 2006 22:19:17 -0800 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross++rosswalker.co.uk] Dear Jun, > Do you have any suggestion on how to qualitatively estimate > the bandwidth of absorption spectrum given a molecular > structure? Can factors affecting the bandwidth be calculated > practically (for instance, molecule with 20 heavy atoms)? The following papers detail a QM/MM MD method for calculating absorption and emission spectra with widths - you may find them useful: Walker, R.C., et al., J. Phys. Chem. B., 2002, 106(44), 11658-11665 Mercer, I.P., et al., J. Phys. Chem. B., 1999, 103, 7720 Mercer, I.P., et al., Faraday Disc., 1997, 51 All the best Ross /\ \/ |\oss Walker | HPC Consultant and Staff Scientist | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross(0)rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. From owner-chemistry@ccl.net Fri Mar 24 11:24:01 2006 From: "Roger Kevin Robinson r.robinson::imperial.ac.uk" To: CCL Subject: CCL: Wireless cluster Message-Id: <-31312-060324104939-6062-6cwTnnXz5SpwvuxTkRdOXA]*[server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 24 Mar 2006 15:45:47 +0000 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson . imperial.ac.uk] I dont really know how much data you need to be moving about so im not sure if it can be done, but do you have a wireless network at home ? I've had two wireless router and they are a pain in the bum. If you were going to do this I would suggest you brought top of the range wireless gear if you expected it to stay connected. To be honest I dont think most wireless cards being produced today would be able to cope with staying connected. Plus isnt the bandwidth on the hub spilt unlike with wires. Ie a port port wired hub 100mbits is 4x100mbit. But a wireless access point is 54/108mbits max doesnt matter how many people are connected, I think. Roger John McKelvey jmmckel%x%attglobal.net wrote: >Sent to CCL by: John McKelvey [jmmckel!^!attglobal.net] >Cheers! > >Please don't laugh, or maybe this is so funny [ridiculous?] that you'll >get a good laugh, and it will make your day! > >Anyway, I want to build a small linux cluster [6-8 total processors] but >don't have a lot of cooling in one place. Running wires would not be >practical, if not impossible Now, the application is extremely >coarse-grain, and only a very, very small amount of data gets moved >about once initialization of a job is done.. Can it be done "wireless?" > >Please share your laughs... > >Cheers.. >John McKelvey> > > > > From owner-chemistry@ccl.net Fri Mar 24 12:08:00 2006 From: "John Daily john.daily~!~colorado.edu" To: CCL Subject: CCL: Contour Plots Message-Id: <-31313-060324113940-8538-sUU5tcJaMlnVVoPY6b7vdQ!^!server.ccl.net> X-Original-From: John Daily Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 24 Mar 2006 09:06:38 -0700 Mime-Version: 1.0 (Apple Message framework v746.3) Sent to CCL by: John Daily [john.daily-*-colorado.edu] I use Igor Pro for almost all my plotting needs. It does contour plots as well as many other types of plots. It is available for PC and Mac. http://www.wavemetrics.com/ John From owner-chemistry@ccl.net Fri Mar 24 12:43:00 2006 From: "Grigori Sigalov sigalov|a|vt.edu" To: CCL Subject: CCL: how to make psfgen input for estrogen receptor Message-Id: <-31314-060324035250-15666-GEcRoDcxk3esp/mdQRMMMQ * server.ccl.net> X-Original-From: Grigori Sigalov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1" Date: Thu, 23 Mar 2006 15:43:01 -0500 Mime-Version: 1.0 Sent to CCL by: Grigori Sigalov [sigalov^^^vt.edu] Ira, >error duplicate residue 263 >. >error duplicate residue 436 Look into your PDB files, what are residues 263 and 436? What segments are they in? Any chance they ARE duplicate (same number appears twice)? Greg. -- Beckman Institute, University of Illinois at Urbana-Champaign. Note my other email addresses: greg+*+ks.uiuc.edu, greg_sigalov+*+yahoo.com, sigalov+*+inbox.ru. From owner-chemistry@ccl.net Fri Mar 24 13:17:01 2006 From: "Ross Walker ross^rosswalker.co.uk" To: CCL Subject: CCL: Wireless cluster Message-Id: <-31315-060324120510-23501-Wlrvp6RtRJ4Oo3vt5/2PKA%a%server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 24 Mar 2006 09:05:02 -0800 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross%rosswalker.co.uk] Dear John, > Anyway, I want to build a small linux cluster [6-8 total > processors] but > don't have a lot of cooling in one place. Running wires > would not be > practical, if not impossible Now, the application is extremely > coarse-grain, and only a very, very small amount of data gets moved > about once initialization of a job is done.. Can it be done > "wireless?" In principle there is no reason why you can't do this, although with some caveats. The first is that each machine will likely have to have its own local disk and operating system as you won't be able to remote boot over a wireless adapter. You should also probably install the software locally on each machine to limit NFS read and writes. Assuming that your simulations really will be extremely course grain then you should be fine with this setup. I would avoid any kind of MPI communications if you can as the performance of these types of communications will not be good. Wireless bandwidth can be okay as long as only one machine communicates at a time so if your jobs will communicate in an asynchronous fashion, with regards to read and writes over the wireless network then it won't be too bad, however, if they all try to read and write at the same time the network performance will be severely limited. The only other thing you need to be aware of is security, obviously with the machines hooked up on a wireless network you will need to think carefully about any security considerations, how to secure the network and/or the machines. All the best Ross /\ \/ |\oss Walker | HPC Consultant and Staff Scientist | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross#%#rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. From owner-chemistry@ccl.net Fri Mar 24 13:52:00 2006 From: "Andrew D. Fant fant-$-pobox.com" To: CCL Subject: CCL: Wireless cluster Message-Id: <-31316-060324122201-31682-JulwBGzs4E1ASkLE0T+sNw:_:server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 24 Mar 2006 12:21:48 -0500 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant=-=pobox.com] John McKelvey jmmckel%x%attglobal.net wrote: > > Please don't laugh, or maybe this is so funny [ridiculous?] that you'll > get a good laugh, and it will make your day! > > Anyway, I want to build a small linux cluster [6-8 total processors] but > don't have a lot of cooling in one place. Running wires would not be > practical, if not impossible Now, the application is extremely > coarse-grain, and only a very, very small amount of data gets moved > about once initialization of a job is done.. Can it be done "wireless?" Hey John, I wouldn't make it my first solution, but it could be done. As others have pointed out, your bandwidth would be limited, your latency would be rather variable, and you would be stuck in half-duplex mode for your communications. You might want to look at more sophisticated methods for data transmission to make up for this if the process isn't truly embarrassingly parallel. In particular, coding with MPI even if it isn't strictly required for the parallelism might pay dividends, since you would be able to use gather/scatter and broadcast/reduce code to sling what data you have around, which might be more efficient than what you can do from the shell. Alternately, if you break down and get a good wireless router that supports multicast well, you might want to look at using multicast to handle communications. Again, the idea being to announce data that other systems might care about and let the ones that actually DO care grab it from one set of packets. Then again, they are doing wonders with pantone-matched drop cables and discrete baseboard mounting clips these days, too. ;-) Hope this helps, Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant##pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Fri Mar 24 14:27:00 2006 From: "Carlos Silva Lopez csilval#,#uvigo.es" To: CCL Subject: CCL: Wireless cluster Message-Id: <-31317-060324115906-21448-6wKlPeCehOBljORFADvong(-)server.ccl.net> X-Original-From: Carlos Silva Lopez Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 24 Mar 2006 17:15:24 +0100 MIME-Version: 1.0 Sent to CCL by: Carlos Silva Lopez [csilval * uvigo.es] Yes it could, but take into account that wireless card get really hot either, so you might be in a safer side with wires John McKelvey jmmckel%x%attglobal.net wrote: >Sent to CCL by: John McKelvey [jmmckel!^!attglobal.net] >Cheers! > >Please don't laugh, or maybe this is so funny [ridiculous?] that you'll >get a good laugh, and it will make your day! > >Anyway, I want to build a small linux cluster [6-8 total processors] but >don't have a lot of cooling in one place. Running wires would not be >practical, if not impossible Now, the application is extremely >coarse-grain, and only a very, very small amount of data gets moved >about once initialization of a job is done.. Can it be done "wireless?" > >Please share your laughs... > >Cheers.. >John McKelvey> > > > > -- Dr. Carlos Silva Lopez Fac. Ciencias Dpt. Quimica Organica Lagoas (Marcosende) s/n Universidade de Vigo web: riesling.chem.umn.edu/~carlos Researcher voice: +34986813721 From owner-chemistry@ccl.net Fri Mar 24 15:02:00 2006 From: "Ray Merewether Ray_Merewether[#]deepsea.com" To: CCL Subject: CCL: How to create a b&w contour plot containing a cutout Message-Id: <-31318-060324093223-681-ed08AOL+UMvUd2a7tvtIdQ-,-server.ccl.net> X-Original-From: "Ray Merewether" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 24 Mar 2006 05:45:03 -0800 MIME-Version: 1.0 Sent to CCL by: "Ray Merewether" [Ray_Merewether*o*deepsea.com] In Matlab, you can use NaN (Not A Number) to cut holes in surf(), surfc() and contour() plots. Octave should be similar. -----Original Message----- > From: owner-chemistry-.-ccl.net [mailto:owner-chemistry-.-ccl.net] Sent: Friday, March 24, 2006 2:08 AM To: Ray Merewether Subject: CCL: How to create a b&w contour plot containing a cutout Sent to CCL by: Anselm.Horn^chemie.uni-erlangen.de Dear all, I'm sorry, if this is a bit off-topic. When looking for a way to visualize the electrostatic potential of planar systems, one very often finds black&white contour plots, one in the plane, one above (e.g. Ford&Wang, J. Comput. Chem. 1993, 14, 1101-1111). Does anybody know a program that could create such graphics from 2D raw data? Of course, I tried gnuplot, but I faced the following problem: The property values in the plane near the atomic cores were omitted in the above paper, and in the contour plot graphic the lewis structure of the molecule is shown there. However, I cannot tell gnuplot to omit the respective data, because it needs a complete set of rows and columns. On the other hand, if one simply sets the values, that are to omit, to a very high or low constant, the countour lines near the molecular border are probably not correctly calculated (or am I wrong?). The same problems arise with xmgrace, unfortunately. Any hints are welcome! Best regards, Anselm Horn Computer-Chemie-Centrum Friedrich-Alexander-Universitaet Erlangen-Nuernberg Germanyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Mar 24 15:37:00 2006 From: "TJ O Donnell tjo : acm.org" To: CCL Subject: CCL: Wireless cluster Message-Id: <-31319-060324132548-10147-LTI9w/B9tdIDqoIDJv3v/A-$-server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 24 Mar 2006 09:39:04 -0800 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo(!)acm.org] Oh yes it can be done. I have a ray-tracing program that divides up the pixels to process among N processors. It is also very coarse grained, transferring a big load of data up front, then collecting dribs and drabs over many hours/days. My network is a mix of wired and wireless (2 Windows and 3 Linux) and I routinely do this without a hitch. TJ O'Donnell www.gnova.com John McKelvey jmmckel%x%attglobal.net wrote: > Sent to CCL by: John McKelvey [jmmckel!^!attglobal.net] > Cheers! > > Please don't laugh, or maybe this is so funny [ridiculous?] that you'll > get a good laugh, and it will make your day! > > Anyway, I want to build a small linux cluster [6-8 total processors] but > don't have a lot of cooling in one place. Running wires would not be > practical, if not impossible Now, the application is extremely > coarse-grain, and only a very, very small amount of data gets moved > about once initialization of a job is done.. Can it be done "wireless?" > > Please share your laughs... > > Cheers.. > John McKelvey> > From owner-chemistry@ccl.net Fri Mar 24 17:03:00 2006 From: "John Hearns john.hearns:+:streamline-computing.com" To: CCL Subject: CCL: Wireless cluster Message-Id: <-31320-060324165950-10680-ZYTHldgG3BcBP2czlrZ18Q%x%server.ccl.net> X-Original-From: John Hearns Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 24 Mar 2006 21:20:21 +0000 Mime-Version: 1.0 Sent to CCL by: John Hearns [john.hearns(!)streamline-computing.com] On Fri, 2006-03-24 at 09:21 -0500, John McKelvey jmmckel%x%attglobal.net wrote: > > Anyway, I want to build a small linux cluster [6-8 total processors] but > don't have a lot of cooling in one place. Running wires would not be > practical, if not impossible Now, the application is extremely > coarse-grain, and only a very, very small amount of data gets moved > about once initialization of a job is done.. Can it be done "wireless?" > Ideas for this have been kicked around by Jim Lux of Caltech on the Beowulf list. >From the networking point of view, the main problem would be PXE booting via wireless. So just do a fixed install on each node. Interesting concept. From owner-chemistry@ccl.net Fri Mar 24 17:37:01 2006 From: "Pankaj Daga pdaga=-=olemiss.edu" To: CCL Subject: CCL: how to choose the bioactive conformation for CoMFA? Message-Id: <-31321-060324163941-6197-w54ZkMXt2qe0qJoD5Qe+qw- -server.ccl.net> X-Original-From: "Pankaj Daga" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 24 Mar 2006 08:59:56 -1200 MIME-Version: 1.0 Sent to CCL by: "Pankaj Daga" [pdaga+*+olemiss.edu] IN many cases, if the bioactive conformation is not available, the minimum energy conformation is considered to be the bioactive conformation. Minimum energy conformation can be obtained by conformational search of the molecule. Cheers panda > Sent to CCL by: "Shobe, David" [dshobe||sud-chemieinc.com] > C Sakthivel wrote: > > How do I choose the bioactive conformation of a > > perticular compound if such type of compounds were not > investigated earlier? > > I'd be surprised if there were a general method for > this...it all depends on which proteins it's supposed to > interact with (the bioactive conformation would be > whichever conformation fits the protein better), and it > doesn't sound like you have that information. > > > --David Shobe, Ph.D., M.L.S. > Süd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > > > -----Original Message----- > > From: owner-chemistry()ccl.net > [mailto:owner-chemistry()ccl.net] Sent: Wednesday, March > 22, 2006 6:48 PM To: Shobe, David > Subject: CCL: how to choose the bioactive conformation for > CoMFA? > > Sent to CCL by: Sakthivel C [skvchem[]yahoo.com] > --0-882663183-1143036218=:29550 Content-Type: text/plain; > charset=iso-8859-1 Content-Transfer-Encoding: 8bit > > Dear CCLers, > I'm working on 3D QSAR studies of some ancancer drugs > that are developed in our lab. Former members of our > group synthesized & studied the ancancer activity for > those compounds. I want to use the activity data for my > 3D QSAR studies (CoMFA & CoMSIA) and identify some new > compounds in same series. I learnt that choosing a wrong > bioactive conformer would lead to worng results. > So, my question is > How do I choose the bioactive conformation of a > perticular compound if such type of compounds were not > investigated earlier? > > Can any one suggest me? > > Looking forward to hear from you. > > Sincerely, > > C Sakthivel > Bharathidasan University > India > > > C. SAKTHIVEL > Research Scholar > School of Chemistry > Bharathidsan University > Tiruchirappalli 620 024 > TN, India > E-mail: skvchem~!~yahoo.com > skv_chem~!~yahoo.co.in > > > > > --------------------------------- > Yahoo! Mail > Use Photomail to share photos without annoying > attachments. --0-882663183-1143036218=:29550 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
Dear CCLers,
I'm working on 3D QSAR > studies of some ancancer drugs that are developed in our > lab. Former members of our group synthesized & > studied the ancancer activity for those compounds. I > want to use the activity data for my 3D QSAR studies > (CoMFA & CoMSIA) and identify some new compounds > in same series. I learnt that choosing a wrong > bioactive conformer would lead to worng results. >
So, my question is
How > do I choose the bioactive conformation of a perticular > compound if such type of compounds were not > investigated earlier?
>
Can any one suggest me?
>
Looking forward to hear from you.
> ;
Sincerely,
C > Sakthivel
Bharathidasan University
>
India


color=#00007f>C. SAKTHIVEL FONT>
Research > Scholar
color=#ff007f>School of Chemistry
face=arial color=#ff007f>Bharathidsan > University
color=#ff007f>Tiruchirappalli 620 024
>
TN, India
> >

>

Yahoo! Mail
> href="http://pa.yahoo.com/*http://us.rd.yahoo.com/evt=3886 > 7/*http://photomail.mail.yahoo.com">Use Photomail to > share photos without annoying attachments. > --0-882663183-1143036218=:29550--http://www.ccl.net/cgi-bi > n/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_uns > ub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message > may contain confidential and / or privileged information. > If you are not an addressee or otherwise authorized to > receive this message, you should not use, copy, disclose > or take any action based on this e-mail or any information > contained in the message. If you have received this > material in error, please advise the sender immediately by > reply e-mail and delete this message. Thank you. > > > > -= 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> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+-+-+ > > > > Pankaj R. Daga Department of Medicinal Chemistry School of Pharmacy 417 Faser Hall University of Mississippi University, MS, 38677-1848 USA From owner-chemistry@ccl.net Fri Mar 24 18:23:00 2006 From: "Venkatnathan, Arun arun.venkatnathan||pnl.gov" To: CCL Subject: CCL: Amorphous Structure Builder Message-Id: <-31322-060324142049-19200-XfaojYv1GS1uykLLfKXHLg(_)server.ccl.net> X-Original-From: "Venkatnathan, Arun" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=iso-8859-1 Date: Fri, 24 Mar 2006 09:53:02 -0800 MIME-version: 1.0 Sent to CCL by: "Venkatnathan, Arun" [arun.venkatnathan%a%pnl.gov] Dear CCLers, I am trying to build a huge amorphous polymer (around 2500 atoms at atleast) using different monomers and will need suggestions on what software is the best. Alternatively, I think the same build can be achieved using Monte Carlo. Does anyone have a Monte Carlo code in Fortran willing to give me which can construct this polymer using different monomers? Thanks - Arun - From owner-chemistry@ccl.net Fri Mar 24 20:02:01 2006 From: "Dominic Ryan dominic.ryan,,comcast.net" To: CCL Subject: CCL: how to choose the bioactive conformation for CoMFA? Message-Id: <-31323-060324193610-32718-hiR/g/PxkWBPXW6a1qx+Gg:server.ccl.net> X-Original-From: "Dominic Ryan" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 24 Mar 2006 18:57:49 -0500 MIME-Version: 1.0 Sent to CCL by: "Dominic Ryan" [dominic.ryan _ comcast.net] It is important to realize that there are usually a reasonably large number of low energy conformations and that picking the lowest is no assurance that you have picked the relevant one. In addition, one has to worry about lowest *free* energy, and in the right environment, not simple mechanics minimization. Dominic Ryan -----Original Message----- > From: owner-chemistry-x-ccl.net [mailto:owner-chemistry-x-ccl.net] Sent: Friday, March 24, 2006 5:55 PM To: Ryan, M Dominic Subject: CCL: how to choose the bioactive conformation for CoMFA? Sent to CCL by: "Pankaj Daga" [pdaga+*+olemiss.edu] IN many cases, if the bioactive conformation is not available, the minimum energy conformation is considered to be the bioactive conformation. Minimum energy conformation can be obtained by conformational search of the molecule. Cheers panda > Sent to CCL by: "Shobe, David" [dshobe||sud-chemieinc.com] > C Sakthivel wrote: > > How do I choose the bioactive conformation of a > > perticular compound if such type of compounds were not > investigated earlier? > > I'd be surprised if there were a general method for > this...it all depends on which proteins it's supposed to > interact with (the bioactive conformation would be > whichever conformation fits the protein better), and it > doesn't sound like you have that information. > > > --David Shobe, Ph.D., M.L.S. > Süd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > > > -----Original Message----- > > From: owner-chemistry()ccl.net > [mailto:owner-chemistry()ccl.net] Sent: Wednesday, March > 22, 2006 6:48 PM To: Shobe, David > Subject: CCL: how to choose the bioactive conformation for > CoMFA? > > Sent to CCL by: Sakthivel C [skvchem[]yahoo.com] > --0-882663183-1143036218=:29550 Content-Type: text/plain; > charset=iso-8859-1 Content-Transfer-Encoding: 8bit > > Dear CCLers, > I'm working on 3D QSAR studies of some ancancer drugs > that are developed in our lab. Former members of our > group synthesized & studied the ancancer activity for > those compounds. I want to use the activity data for my > 3D QSAR studies (CoMFA & CoMSIA) and identify some new > compounds in same series. I learnt that choosing a wrong > bioactive conformer would lead to worng results. > So, my question is > How do I choose the bioactive conformation of a > perticular compound if such type of compounds were not > investigated earlier? > > Can any one suggest me? > > Looking forward to hear from you. > > Sincerely, > > C Sakthivel > Bharathidasan University > India > > > C. SAKTHIVEL > Research Scholar > School of Chemistry > Bharathidsan University > Tiruchirappalli 620 024 > TN, India > E-mail: skvchem~!~yahoo.com > skv_chem~!~yahoo.co.in > > > > > --------------------------------- > Yahoo! Mail > Use Photomail to share photos without annoying > attachments. --0-882663183-1143036218=:29550 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
Dear CCLers,
I'm working on 3D QSAR > studies of some ancancer drugs that are developed in our > lab. Former members of our group synthesized & > studied the ancancer activity for those compounds. I > want to use the activity data for my 3D QSAR studies > (CoMFA & CoMSIA) and identify some new compounds > in same series. I learnt that choosing a wrong > bioactive conformer would lead to worng results. >
So, my question is
How > do I choose the bioactive conformation of a perticular > compound if such type of compounds were not > investigated earlier?
>
Can any one suggest me?
>
Looking forward to hear from you.
> ;
Sincerely,
C > Sakthivel
Bharathidasan University
>
India


color=#00007f>C. SAKTHIVEL FONT>
Research > Scholar
color=#ff007f>School of Chemistry
face=arial color=#ff007f>Bharathidsan > University
color=#ff007f>Tiruchirappalli 620 024
>
TN, India
> >

>

Yahoo! Mail
> href="http://pa.yahoo.com/*http://us.rd.yahoo.com/evt=3886 > 7/*http://photomail.mail.yahoo.com">Use Photomail to > share photos without annoying attachments. > --0-882663183-1143036218=:29550--http://www.ccl.net/cgi-bi > n/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_uns > ub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message > may contain confidential and / or privileged information. > If you are not an addressee or otherwise authorized to > receive this message, you should not use, copy, disclose > or take any action based on this e-mail or any information > contained in the message. If you have received this > material in error, please advise the sender immediately by > reply e-mail and delete this message. Thank you. > > > > -= 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> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+-+-+ > > > > Pankaj R. Daga Department of Medicinal Chemistry School of Pharmacy 417 Faser Hall University of Mississippi University, MS, 38677-1848 USAhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt