From owner-chemistry@ccl.net Tue Dec 2 07:35:00 2008 From: "Mahmoud Korani Abdel-Latif mkkhedr:+:hotmail.com" To: CCL Subject: CCL: XYZ Coordinate Shift (Thanks) Message-Id: <-38217-081202073328-1401-rIOMkiC5z4nv1eQeEmh0GQ===server.ccl.net> X-Original-From: "Mahmoud Korani Abdel-Latif" Date: Tue, 2 Dec 2008 07:33:24 -0500 Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr=hotmail.com] Dear All, Great thanks for your interest and I really appreciate your help. Best regards, Mahmoud From owner-chemistry@ccl.net Tue Dec 2 08:54:01 2008 From: "Harry Stern hstern16,,mac.com" To: CCL Subject: CCL: Ewald sum Message-Id: <-38218-081201221058-3302-BQi/b3kuMDxR9NvKKt1zxA:+:server.ccl.net> X-Original-From: Harry Stern Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Mon, 01 Dec 2008 21:10:21 -0500 MIME-version: 1.0 Sent to CCL by: Harry Stern [hstern16- -mac.com] Another test is to use a small test system, and a larger test system constructed from the original + periodic copies. e.g if simple cubic boundary conditions are used, a 2x2x2 system with 8 times the volume of the original small system can be constructed. If the code is correct and Ewald parameters are chosen such that the calculation is accurate, the energy for the large system should be very close to 8 times the energy for the small original system. Harry Stern On Dec 1, 2008, at 9:57 AM, Mihaly Mezei Mihaly.Mezei(~)mssm.edu wrote: > > Sent to CCL by: Mihaly Mezei [Mihaly.Mezei-,-mssm.edu] > > >> I have recieved some result for my Ewald sum code, However I don't >> know if they are correct or not. Can you please advise me how to >> evaluate my results? >> > Onesuch test is that the result should be the same with different > weights given to the direct and reciprocal spacecontribution. > > Mihaly Mezei > > Department of Structural and Chemical Biology, Mount Sinai School of > Medicine, NYU > Voice: (212) 659-5475 Fax: (212) 849-2456 > WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > WWW (Department): http://atlas.physbio.mssm.edu > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > From owner-chemistry@ccl.net Tue Dec 2 09:35:01 2008 From: "Iain Wallace iain.m.wallace _ gmail.com" To: CCL Subject: CCL: Lead optimization Message-Id: <-38219-081202093354-19603-/2Yjx9iXqY0OgxKNhFzDng()server.ccl.net> X-Original-From: "Iain Wallace" Content-Type: multipart/alternative; boundary="----=_Part_72978_10474063.1228228419187" Date: Tue, 2 Dec 2008 09:33:39 -0500 MIME-Version: 1.0 Sent to CCL by: "Iain Wallace" [iain.m.wallace]|[gmail.com] ------=_Part_72978_10474063.1228228419187 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all, I was wondering if anybody could give me some basic pointers on lead optimizations. First of all, is there any (free) software that will propose interesting analogues to make/buy, and give a rationalization for proposing them And also, does any one know of any reviews or books that explains the lead optimization process? I would really like to find something with worked examples Thanks a million, Cheers Iain ------=_Part_72978_10474063.1228228419187 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all,

I was wondering if anybody could give me some basic pointers on lead optimizations.
First of all,  is there any (free) software that will propose interesting analogues to make/buy, and give a rationalization for proposing them
And also, does any one know of any reviews or books that explains the lead optimization process? I would really like to find something with worked examples

Thanks a million,

Cheers

Iain
------=_Part_72978_10474063.1228228419187-- From owner-chemistry@ccl.net Tue Dec 2 12:28:01 2008 From: "Johannes Kreutzer kreutzer^^sbox.tugraz.at" To: CCL Subject: CCL:G: Error report: the smallest beta delta epsilon is... Message-Id: <-38220-081202084609-31469-B6iIRa4vPvLxYAGv1Hxl9Q-$-server.ccl.net> X-Original-From: Johannes Kreutzer Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Tue, 02 Dec 2008 13:55:25 +0100 MIME-Version: 1.0 Sent to CCL by: Johannes Kreutzer [kreutzer]=[sbox.tugraz.at] Dear CCLers, I have a problem with calculating the excitation of Europium. I start the calculation on the TD-B3LYP level and use the Stuttgard Dresden Basis Sets (28mwb, 52mwb and 52mhf) published by Dolg. After the SCF iteration i get the following error report: Leave Link 502 at Mon Dec 1 14:37:04 2008, MaxMem= 134217728 cpu: 0.9 (Enter /usr/local/g03/l801.exe) Range of M.O.s used for correlation: 1 32 NBasis= 32 NAE= 9 NBE= 2 NFC= 0 NFV= 0 NROrb= 32 NOA= 9 NOB= 2 NVA= 23 NVB= 30 **** Warning!!: The smallest alpha delta epsilon is 0.46415712D-01 **** Fatal Problem: The smallest beta delta epsilon is 0.99920072D-15 Error termination via Lnk1e in /usr/local/g03/l801.exe at Mon Dec 1 14:37:05 2008. Does anybody has experience with that? Did anybody find the same problem? Kind regards johannes Kreutzer From owner-chemistry@ccl.net Tue Dec 2 13:03:00 2008 From: "Tom Walsh tom===compbio.dundee.ac.uk" To: CCL Subject: CCL:G: Gaussian 03 on CentOS 5.2 Message-Id: <-38221-081202065654-29688-JlIneMCaW8AOmX7tfEcuhw|-|server.ccl.net> X-Original-From: "Tom Walsh" Date: Tue, 2 Dec 2008 06:56:50 -0500 Sent to CCL by: "Tom Walsh" [tom^compbio.dundee.ac.uk] Hi, Does anyone have experience of running Gaussian 03 on CentOS 5.2 (on 64-bit Intel Xeon CPUs)? Gaussian doesn't officially support this OS; the closest supported OS is RHEL 5 (first update) and I'm wondering if the RHEL5 binary will run OK on CentOS 5.2. The alternative is to build it from source but I don't know if there would be issues with that also. Unfortunately using a supported OS is not an option. Thanks, Tom Walsh From owner-chemistry@ccl.net Tue Dec 2 13:37:01 2008 From: "Vincent Leroux vincent.leroux ~~ loria.fr" To: CCL Subject: CCL: Lead optimization Message-Id: <-38222-081202122846-32329-bc2gnNhguOl/f2xFqn4yQw##server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 02 Dec 2008 17:34:24 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux|*|loria.fr] Hi Iain, Depends of what you have at this stage. Crystal / NMR structures of complexes, or model structures, or none? Were mutagenesis experiments performed? If there is a target structural model involved, was its conformational space explored, with normal modes analysis / molecular dynamics? You might have biological activity measurements already, but on how much compounds? Are the assays reliable? Were SAR studies done? Were trials of any kind conducted? etc. There are numerous lead optimization strategies to choose from, answering the above questions could determine which ones are available to you mostly by eliminating the ones that are not. You might also want to check what amount of effort / manwork you can investigate, what tools are available to you, and in which fields that can be involved in the drug design process (biology, lab chemistry, theoretical chemistry, computer science...). You should specify this somewhat so that the related specialists here will be able to help you. VL Iain Wallace iain.m.wallace _ gmail.com a écrit : > Hi all, > > I was wondering if anybody could give me some basic pointers on lead > optimizations. > First of all, is there any (free) software that will propose > interesting analogues to make/buy, and give a rationalization for > proposing them > And also, does any one know of any reviews or books that explains the > lead optimization process? I would really like to find something with > worked examples > > Thanks a million, > > Cheers > > Iain From owner-chemistry@ccl.net Tue Dec 2 14:53:00 2008 From: "Adam Tenderholt atenderholt-*-gmail.com" To: CCL Subject: CCL:G: Gaussian 03 on CentOS 5.2 Message-Id: <-38223-081202144842-28330-OGxx4Xkhwe3OfkUx/5rkeQ##server.ccl.net> X-Original-From: "Adam Tenderholt" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 2 Dec 2008 11:48:31 -0800 MIME-Version: 1.0 Sent to CCL by: "Adam Tenderholt" [atenderholt[*]gmail.com] Hi Tom, I recently setup a Rocks cluster, which is running CentOS 5.2, on a handful of 32-bit Intel Xeons. I managed to get Gaussian 03 to work once I found the a page detailing some setting I needed to change to a running kernel. The command and page are: echo 0 > /proc/sys/kernel/randomize_va_space http://www.ccl.net/chemistry/resources/messages/2008/01/22.004-dir/index.html Adam On Tue, Dec 2, 2008 at 3:56 AM, Tom Walsh tom===compbio.dundee.ac.uk wrote: > > Sent to CCL by: "Tom Walsh" [tom^compbio.dundee.ac.uk] > Hi, > > Does anyone have experience of running Gaussian 03 on CentOS 5.2 (on 64-bit Intel Xeon CPUs)? Gaussian doesn't officially support this OS; the closest supported OS is RHEL 5 (first update) and I'm wondering if the RHEL5 binary will run OK on CentOS 5.2. The alternative is to build it from source but I don't know if there would be issues with that also. Unfortunately using a supported OS is not an option. > > Thanks, > > Tom Walsh> > > From owner-chemistry@ccl.net Tue Dec 2 15:28:01 2008 From: "Daniel Jana dfjana++gmail.com" To: CCL Subject: CCL:G: Gaussian 03 on CentOS 5.2 Message-Id: <-38224-081202145632-30286-Qw0ZmFsuct8Yi8MCTfh6OQ=-=server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 02 Dec 2008 20:55:54 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana-#-gmail.com] Hello, Tom Walsh tom===compbio.dundee.ac.uk wrote: > Does anyone have experience of running Gaussian 03 on CentOS 5.2 (on 64-bit Intel Xeon CPUs)? Gaussian doesn't officially support this OS; the closest supported OS is RHEL 5 (first update) and I'm wondering if the RHEL5 binary will run OK on CentOS 5.2. The alternative is to build it from source but I don't know if there would be issues with that also. Unfortunately using a supported OS is not an option. > $ cat /etc/redhat-release CentOS release 5.2 (Final) $ cat /proc/cpuinfo processor : 0 vendor_id : AuthenticAMD cpu family : 16 model : 2 model name : Quad-Core AMD Opteron(tm) Processor 2352 (...) The cpu is not the one you asked for, but we have been using the same OS without any problems. We are using Gaussian03 E.01, the latest version. Best, Daniel Jana From owner-chemistry@ccl.net Tue Dec 2 16:02:00 2008 From: "Igor Filippov Contr igorf###helix.nih.gov" To: CCL Subject: CCL:G: Gaussian 03 on CentOS 5.2 Message-Id: <-38225-081202144420-28068-r0WtUc0cu3KQJ0sCan23UQ]_[server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 02 Dec 2008 14:10:49 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf-#-helix.nih.gov] I have compiled g03 E01 on CentOs 4.4 AMD64 system. Here are my notes for the process: csh setenv PGI /usr/pgi setenv PATH ${PATH}:${PGI}/linux86-64/5.1/bin setenv g03root /root/g03-E01-amd64 edit set-mflags and setup-make to remove mcmodel=medium edit i386.make to pick amd64 BLAS libraries ./bsd/install source $g03root/g03/bsd/g03.login bsd/bldg03 Hope this helps, Igor On Tue, 2008-12-02 at 06:56 -0500, Tom Walsh tom===compbio.dundee.ac.uk wrote: > Sent to CCL by: "Tom Walsh" [tom^compbio.dundee.ac.uk] > Hi, > > Does anyone have experience of running Gaussian 03 on CentOS 5.2 (on 64-bit Intel Xeon CPUs)? Gaussian doesn't officially support this OS; the closest supported OS is RHEL 5 (first update) and I'm wondering if the RHEL5 binary will run OK on CentOS 5.2. The alternative is to build it from source but I don't know if there would be issues with that also. Unfortunately using a supported OS is not an option. > > Thanks, > > Tom Walsh> From owner-chemistry@ccl.net Tue Dec 2 16:38:00 2008 From: "Steve Williams willsd[*]appstate.edu" To: CCL Subject: CCL:G: Gaussian 03 on CentOS 5.2 Message-Id: <-38226-081202144619-28204-npaEEgkIzIjXbLvJfIMzTQ^^^server.ccl.net> X-Original-From: Steve Williams Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 02 Dec 2008 14:36:55 -0500 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd-$-appstate.edu] I have installed a licensed intel linux 64 (intel em64t) version of gaussian 03 (with Linda) on a PQS computer (running centos 5) that has 2 quadcore xeons per node and 2 nodes. It runs great on 8 processors with %nprocshared=8 and quite well on all 16 processors using Linda for internode communications with %nprocshared=8 and %nprocLinda=2. I am by no means a linux expert, but I did not have any significant problems with the install. Steve Williams Tom Walsh tom===compbio.dundee.ac.uk wrote: > Sent to CCL by: "Tom Walsh" [tom^compbio.dundee.ac.uk] > Hi, > > Does anyone have experience of running Gaussian 03 on CentOS 5.2 (on 64-bit Intel Xeon CPUs)? Gaussian doesn't officially support this OS; the closest supported OS is RHEL 5 (first update) and I'm wondering if the RHEL5 binary will run OK on CentOS 5.2. The alternative is to build it from source but I don't know if there would be issues with that also. Unfortunately using a supported OS is not an option. > > Thanks, > > Tom Walsh> > > From owner-chemistry@ccl.net Tue Dec 2 19:56:01 2008 From: "Iain Wallace iain.m.wallace/./gmail.com" To: CCL Subject: CCL: Lead optimization Message-Id: <-38227-081202183659-12995-+HF+lwUIQ0EtVU2c9Zvxxw#%#server.ccl.net> X-Original-From: "Iain Wallace" Content-Type: multipart/alternative; boundary="----=_Part_78601_32964399.1228261005980" Date: Tue, 2 Dec 2008 18:36:45 -0500 MIME-Version: 1.0 Sent to CCL by: "Iain Wallace" [iain.m.wallace__gmail.com] ------=_Part_78601_32964399.1228261005980 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Vincent, Thanks for your reply. Basically I work in an academic lab and we would lik= e to purchase some interesting analogues of compounds that we have found. So far, we have no structure and no SAR information. I am currently just using a substructure/similarity search to identify compounds. I was wondering if there was anything else out there that might be useful in searching. One thought I had was searching using Bioisosterism= , where a chemical group or fragment is replaced by an equivalent group. What I have found so far is *S*imilarity *i*n *B*io*I*sosteric *S*pace (SiBIS) from http://www.moltop.com/, and Brood from OpenEye The Quantum Isostere Database also look= s very interesting Ideally I would like to find a resource that would explain reasons for making particular chemical substitutions or an automatic way of suggesting them Cheers Iain On Tue, Dec 2, 2008 at 11:34 AM, Vincent Leroux vincent.leroux ~~ loria.fr = < owner-chemistry:ccl.net> wrote: > > Sent to CCL by: Vincent Leroux [vincent.leroux|*|loria.fr] > Hi Iain, > > Depends of what you have at this stage. Crystal / NMR structures of > complexes, or model structures, or none? Were mutagenesis experiments > performed? If there is a target structural model involved, was its > conformational space explored, with normal modes analysis / molecular > dynamics? You might have biological activity measurements already, but on > how much compounds? Are the assays reliable? Were SAR studies done? Were > trials of any kind conducted? etc. > > There are numerous lead optimization strategies to choose from, answering > the above questions could determine which ones are available to you mostl= y > by eliminating the ones that are not. You might also want to check what > amount of effort / manwork you can investigate, what tools are available = to > you, and in which fields that can be involved in the drug design process > (biology, lab chemistry, theoretical chemistry, computer science...). > > You should specify this somewhat so that the related specialists here wil= l > be able to help you. > > VL > > > Iain Wallace iain.m.wallace _ gmail.com a =E9crit : > > Hi all, >> >> I was wondering if anybody could give me some basic pointers on lead >> optimizations. >> First of all, is there any (free) software that will propose interestin= g >> analogues to make/buy, and give a rationalization for proposing them >> And also, does any one know of any reviews or books that explains the le= ad >> optimization process? I would really like to find something with worked >> examples >> >> Thanks a million, >> >> Cheers >> >> Iain >> > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_78601_32964399.1228261005980 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Vincent,

Thanks for your reply. Basically I work in an academic l= ab and we would like to purchase some interesting analogues of compounds th= at we have found. So far, we have no structure and no SAR information.
I am currently just using a substructure/similarity search to identify comp= ounds. I was wondering if there was anything else out there that might be u= seful in searching. One thought I had was searching using Bioisosterism, wh= ere a chemical group or fragment is replaced by an equivalent group.
What I have found so far is = Similarity in BioIsosteric Space (SiBIS) from http://www.moltop.com= /, and Brood from OpenEye
The Quantum Isostere Database also looks very intere= sting

Ideally I would like to find a resource that would explain reasons for = making particular chemical substitutions or an automatic way of suggesting = them

Cheers

Iain

On Tue, D= ec 2, 2008 at 11:34 AM, Vincent Leroux vincent.leroux ~~ loria.fr <owner-chemistry:ccl.net> wrote:

Sent to CCL by: Vincent Leroux [vincent.leroux|*|loria.fr]
Hi Iain,

Depends of what you have at this stage. Crystal / NMR structures of complex= es, or model structures, or none? Were mutagenesis experiments performed? I= f there is a target structural model involved, was its conformational space= explored, with normal modes analysis / molecular dynamics? You might have = biological activity measurements already, but on how much compounds? Are th= e assays reliable? Were SAR studies done? Were trials of any kind conducted= ? etc.

There are numerous lead optimization strategies to choose from, answering t= he above questions could determine which ones are available to you mostly b= y eliminating the ones that are not. You might also want to check what amou= nt of effort / manwork you can investigate, what tools are available to you= , and in which fields that can be involved in the drug design process (biol= ogy, lab chemistry, theoretical chemistry, computer science...).

You should specify this somewhat so that the related specialists here will = be able to help you.

VL


Iain Wallace iain.m.wallace _ gmail.com a =E9crit :

Hi all,

I was wondering if anybody could give me some basic pointers on lead optimi= zations.
First of all,  is there any (free) software that will propose interest= ing analogues to make/buy, and give a rationalization for proposing them And also, does any one know of any reviews or books that explains the lead = optimization process? I would really like to find something with worked exa= mples

Thanks a million,

Cheers

Iain



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