From owner-chemistry@ccl.net Thu Sep 1 13:27:28 2005 From: "CCL" To: CCL Subject: CCL: chemical web services Message-Id: <-29044-050901131340-32180-j6jGbi4IRXakbS2fcikGlA^_^server.ccl.net> X-Original-From: Ferenc Csizmadia Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 01 Sep 2005 19:13:32 +0200 MIME-Version: 1.0 Sent to CCL by: Ferenc Csizmadia [fcsiz^_^chemaxon.com] Hi all, Can anyone direct me to SOAP-based web services that can input chemical structures in a common format (SMILES, CML, Molfile, etc.) and output calculated/predicted properties? Regards, Ferenc PS: Sorry for multiple postings --- Ferenc Csizmadia fcsiz^_^chemaxon.com From owner-chemistry@ccl.net Thu Sep 1 13:27:28 2005 From: "CCL" To: CCL Subject: CCL: W:HELP ON GAUSSIAN Message-Id: <-29043-050901131936-32451-j6jGbi4IRXakbS2fcikGlA^^^server.ccl.net> X-Original-From: "Rafael deSouza Monteiro" Sent to CCL by: "Rafael deSouza Monteiro" [rafaeldesmonteiro^^^yahoo.com.br] Why do my calculations of G03W are interrupted when I run them on Windows XP? My computer is a 1.00 GHz AMD Athlon, with 256 MB RAM and 20GB free disk space. My job is a transition state of CO chemisorbed on small clusters, like Pt10 and Fe11 and I used the modredundant keyword to guess the transition states. I use b3lyp functional with lanl2dz basis set. It is often interrupted on the end of first convergence step, with apparently no cause or error message displayed. Thanks for everybody. From owner-chemistry@ccl.net Thu Sep 1 13:33:43 2005 From: "CCL" To: CCL Subject: CCL: Accelrys Workshops for October Message-Id: <-29045-050901133212-3101-j6jGbi4IRXakbS2fcikGlA-*-server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Thu, 1 Sep 2005 10:32:00 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss-*-accelrys.com] Accelrys Inc. are holding the following training workshops during October 2005. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs for the scheduled workshops are $500 per day for all customers. For the on-line presentations, the price is $175 per three hour session for all customers. PARIS, FRANCE Introduction to Life Science Modeling with Insight II 4-5 Oct Homology-Based Protein Design 6-7 Oct CHARMm 10-11 Oct Structure Based Drug Design with InsightII 12-13 Oct Introduction to DS Modeling 1.1 18-19 Oct Structure Based Drug Design with DS Modeling 1.2 20 Oct ONLINE TRAINING DS ViewerPro 14 October (10 am GMT) Protein-Protein Docking 25 October (7am PDT) Further details can be found on our website at http://www.accelrys.com/training/general/calendar.html and http://www.accelrys.com/training/general/calendar_online.html Questions regarding scheduling and content should be directed to workshops-*-accelrys.com -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training *AccelrysWorld 2005, London, Nov 14-16. http://www.accelrysworld.com* From owner-chemistry@ccl.net Thu Sep 1 14:59:36 2005 From: "CCL" To: CCL Subject: CCL: Help for partial charge of nitrogen atoms in pyrimidine, pyridine and pyrazine Message-Id: <-29046-050901143750-6288-j6jGbi4IRXakbS2fcikGlA]=[server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-645436594-1125596255=:24322" Date: Thu, 1 Sep 2005 12:37:35 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso]=[yahoo.com] --0-645436594-1125596255=:24322 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello, Based on my previous experience (although in systems that have no resemblanace to yours) I believe the electrostatic potential is more meaningful in trying to understand the reactivity than the electron density or the partial charge for that matter. For example, if you take a look to the electronic density in CH3-C=CH it would appear that both sp hybridized C atoms are equaly likely to be atacked by an electrophile, but the electrostatic potential plot is completely coherent with the Markovnikov orientation of an electrophilic adition. Best regards CCL escribió: Hello, Dear CCL'rs: I calculated CHELPG partial charge on nitrogen atoms in pyridine, pyrimidine and pyrazine (also 4-azaindole, 4,6-diazaindole and 4,7-diazaindole) for later binding free energy caculation. Based on their pKa and inductive effect, I would expect that the electron density on nitrogen atoms in pyrimidine or 4,6-diazaindole would be smaller than those in pyridine/4-azaindole. (correct me if I am wrong) However, I got larger partial charge on nitrogen atoms in pyrimidine from gaussian calculation: compound CHELPG partial charge on Nitrogen pKa pridine -0.6043 5.1 pyrimidine ~ -0.77 1.3 pyrazine -0.4395 0.6 I used B3LYP/6-31G(d) basis set in the above calculation. I had tried several other basis sets and charges (Mulliken and Merz-Kollman), and obtained the same obseration. Is my assumption wrong? Please share your experience with me. Thanks in advance for you help! Best wishes, Minghu Song Locus Pharmaceuticals --------------------------------- Start your day with Yahoo! - make it your home page ********************************************************** Q. Joaquín Barroso Flores Instituto de Química UNAM Correo Alterno: joaquin_barroso]=[correo.unam.mx ********************************************************** --------------------------------- Do You Yahoo!? La mejor conexión a Internet y 2GB extra a tu correo por $100 al mes. http://net.yahoo.com.mx --0-645436594-1125596255=:24322 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hello,
 
Based on my previous experience (although in systems that have no resemblanace to yours) I believe the electrostatic potential is more meaningful in trying to understand the reactivity than the electron density or the partial charge for that matter. For example, if you take a look to the electronic density in CH3-C=CH it would appear that both sp hybridized C atoms are equaly likely to be atacked by an electrophile, but the electrostatic potential plot is completely coherent with the Markovnikov orientation of an electrophilic adition.
Best regards
 

CCL <owner-chemistry]=[ccl.net> escribió:
Hello, Dear CCL'rs:
 
I calculated CHELPG partial charge on nitrogen atoms in pyridine, pyrimidine and pyrazine (also 4-azaindole,  4,6-diazaindole and 4,7-diazaindole) for later binding free energy caculation. 
Based on their pKa and inductive effect,  I would expect that the electron density on nitrogen atoms in pyrimidine or 4,6-diazaindole would be smaller than those in pyridine/4-azaindole.  (correct me if I am wrong) However, I got larger partial charge on nitrogen atoms in pyrimidine from gaussian calculation: 
  
compound                CHELPG partial charge on Nitrogen                    pKa
pridine                                  -0.6043                                                5.1
pyrimidine                           ~  -0.77                                                 1.3
pyrazine                               -0.4395                                                0.6
 
I used B3LYP/6-31G(d) basis set in the above calculation.  I had tried several other basis sets and charges (Mulliken and Merz-Kollman), and obtained the same obseration.  Is my assumption wrong?  Please share your experience with me.  Thanks in advance for you help!
 
Best wishes,
 
Minghu Song
Locus Pharmaceuticals

Start your day with Yahoo! - make it your home page


**********************************************************
Q. Joaquín Barroso Flores

Instituto de Química UNAM
Correo Alterno: joaquin_barroso]=[correo.unam.mx
**********************************************************

Do You Yahoo!? La mejor conexión a Internet y 2GB extra a tu correo por $100 al mes. http://net.yahoo.com.mx --0-645436594-1125596255=:24322-- From owner-chemistry@ccl.net Thu Sep 1 15:19:02 2005 From: "CCL" To: CCL Subject: CCL: gamess and amd64 Message-Id: <-29047-050901143014-2767-j6jGbi4IRXakbS2fcikGlA]^[server.ccl.net> X-Original-From: "Felipe Fleming" Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 1 Sep 2005 15:27:36 -0200 MIME-Version: 1.0 Sent to CCL by: "Felipe Fleming" [fleming]^[iq.ufrj.br] Dear sirs, I'm trying to compile gamess (versions june/2004 and july/2005) on an athlon64 running Suse9.3. I've tried the modifications proposed by the compilers dealers, but no luck... I was wondering if anyone managed to get it working under this configuration (athlon64 and SUSE9.3) and could give me a hand! Tank you all very much, Felipe Fleming From owner-chemistry@ccl.net Thu Sep 1 17:08:42 2005 From: "CCL" To: CCL Subject: CCL: N/A Message-Id: <-29048-050901143007-2714-j6jGbi4IRXakbS2fcikGlA]^[server.ccl.net> X-Original-From: "Felipe Fleming" Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 1 Sep 2005 15:27:26 -0200 MIME-Version: 1.0 Sent to CCL by: "Felipe Fleming" [fleming]^[iq.ufrj.br] Dear sirs, I'm trying to compile gamess (versions june/2004 and july/2005) on an athlon64 running Suse9.3. I've tried the modifications proposed by the compilers dealers, but no luck... I was wondering if anyone managed to get it working under this configuration (athlon64 and SUSE9.3) and could give me a hand! Tank you all very much, Felipe Fleming From owner-chemistry@ccl.net Thu Sep 1 17:17:58 2005 From: "CCL" To: CCL Subject: CCL: Autodock: File used to assign charges Message-Id: <-29049-050901171628-29973-j6jGbi4IRXakbS2fcikGlA]|[server.ccl.net> X-Original-From: Tim Janzen Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 01 Sep 2005 15:16:15 -0400 Mime-Version: 1.0 Sent to CCL by: Tim Janzen [tim.janzen]|[uleth.ca] Hi, I have been getting some discrepancies in residue charges when using autodock and was wondering if anyone knew the location of the file that is read to assign these charges to each residue. Thanks, -- Timothy Janzen University of Lethbridge 4401 University Drive Lethbridge AB T1K 3M4 tim.janzen]|[uleth.ca From owner-chemistry@ccl.net Thu Sep 1 20:53:03 2005 From: "CCL" To: CCL Subject: CCL: W:HELP ON GAUSSIAN Message-Id: <-29050-050901205123-1101-j6jGbi4IRXakbS2fcikGlA]=[server.ccl.net> X-Original-From: Jason Thompson Content-Type: multipart/alternative; boundary=Apple-Mail-1--866779783 Date: Thu, 1 Sep 2005 18:19:51 -0500 Mime-Version: 1.0 (Apple Message framework v728) Sent to CCL by: Jason Thompson [Thompson.Jason1]=[mayo.edu] --Apple-Mail-1--866779783 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed This is only a guess, but based on the information you have given, it may be stopping because you have not specified "NoEigentest" within the Opt keyword (see http://www.gaussian.com/g_ur/k_opt.htm, about half way down). For transition state optimizations, I believe the default is "Eigentest", which checks for the correct curvature and stops if it is not correct. Although it is recommended to use "Eigentest" for transition state optimizations, I have found that it is generally not a requirement. But I have never worked with the type of system you are studying. On Sep 1, 2005, at 12:46 PM, CCL wrote: > > Sent to CCL by: "Rafael deSouza > Monteiro" [rafaeldesmonteiro^^^yahoo.com.br] > Why do my calculations of G03W are interrupted when I run them on > Windows > XP? My computer is a 1.00 GHz AMD Athlon, with 256 MB RAM and 20GB > free disk space. > My job is a transition state of CO chemisorbed on small clusters, > like Pt10 and Fe11 and I used the modredundant keyword to guess the > transition states. I use b3lyp functional with lanl2dz basis set. > It is often interrupted on the end of first convergence step, with > apparently no cause or error message displayed. > > Thanks for everybody. > > > > -= This is automatically added to each message by the mailing > script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: CHEMISTRY- > REQUEST]=[ccl.net> > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > Jason D. Thompson, Ph.D. Molecular Pharmacology and Experimental Therapeutics Mayo Clinic Guggenheim 6-93 200 First Street SW Rochester, MN 55905 http://pollux.chem.umn.edu/~thompson --Apple-Mail-1--866779783 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 This is only a guess, but based = on the information you have given, it may be stopping because you have = not specified "NoEigentest" within the Opt keyword (see=A0http://www.gaussian.com/g_= ur/k_opt.htm, about half way down).=A0 For transition state = optimizations, I believe the default is "Eigentest", which checks for = the correct curvature and stops if it is not correct.=A0 Although it is = recommended to use "Eigentest" for transition state optimizations, I = have found that it is generally not a requirement.=A0 But I have never = worked with the type of system you are studying.

On = Sep 1, 2005, at 12:46 PM, CCL wrote:


Sent to = CCL by: "Rafael deSouza Monteiro" = [rafaeldesmonteiro^^^yahoo.com.br]
Why do my = calculations of G03W are interrupted when I run them on = Windows
XP? My computer is a 1.00 GHz = AMD Athlon, with 256 MB RAM and 20GB free disk space.=A0
My job = is a transition state of CO chemisorbed on small clusters, like Pt10 and = Fe11 and I used the modredundant keyword to guess the transition states. = I use b3lyp functional with lanl2dz basis set. It is often interrupted = on the end of first convergence step, with apparently no cause or error = message displayed.
Thanks for everybody.



-=3D This is automatically added = to each message by the mailing script =3D-
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use the Web based form from CCL Home Page=A0



Jason D. Thompson, Ph.D.
Molecular Pharmacology and Experimental = Therapeutics
Mayo Clinic
Guggenheim 6-93
200 First = Street SW
Rochester, MN = 55905

= --Apple-Mail-1--866779783--