From owner-chemistry@ccl.net Fri Sep 2 01:31:12 2005 From: "CCL" To: CCL Subject: CCL: chemical web services Message-Id: <-29051-050902004027-28127-j6jGbi4IRXakbS2fcikGlA!A!server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 01 Sep 2005 21:55:12 -0400 Mime-Version: 1.0 Sent to CCL by: Rajarshi Guha [rxg218!A!psu.edu] On Thu, 2005-09-01 at 19:13 +0200, CCL wrote: > 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? http://blue.chem.psu.edu/~rajarshi/code/java/cdkws.html - there are currently 3 web services available: fingerprints, tanimoto similarity calculation & molecule descriptor calculation. Right now the descriptor service calculates classes of descriptors but this will probably be updated soon to allow specification of specific descriptors for calculation. HTH, ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Does Ramanujan know Polish? -- E.B. Ross From owner-chemistry@ccl.net Fri Sep 2 05:15:43 2005 From: "CCL" To: CCL Subject: CCL: GB+QM with mulliken charges ! Message-Id: <-29052-050902050910-24731-j6jGbi4IRXakbS2fcikGlA:+:server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 2 Sep 2005 14:34:09 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta:+:iitg.ernet.in] Dear All, I am trying to implement Generalized Born with Hartree-Fock thoery using mulliken charges. However, I am getting severe convergence problem. Does anyone have similar experience and know how to overcome that? I would appreciate any response. Pradipta Dr. Pradipta Bandyopadhyay Assistant Professor Dept. of Biotechnology Indian Institute of Technology, Guwahati Phone: 91-361-258-2213 (office) e-mail: pradipta:+:iitg.ernet.in web: http://202.141.80.5/~pradipta/Pradipta.htm ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.in From owner-chemistry@ccl.net Fri Sep 2 08:20:56 2005 From: "CCL" To: CCL Subject: CCL: W:Failed InsightII simulation Message-Id: <-29053-050902014130-4856-j6jGbi4IRXakbS2fcikGlA{=}server.ccl.net> X-Original-From: "Maurizzio Argonni" Sent to CCL by: "Maurizzio Argonni" [m.argonni{=}gmail.com] Hello to all, I am trying to set up a molecular dynamics simulation on aminopeptidase using InsightII but I get an error that I am not sure what to do about. Aminopeptidase (PDB code 1AMP) contains two Zn atoms bridged by an ASP and a water (or OH). Each Zn is complexed by an additional ASP (or GLU) and HIS residues. Because of the Zn atoms I decided to use the esff force field with Discover_3 from within InsightII (version 2000). I pretty much followed the instructions in the CDiscover manual: 1) Load the protein 2) Add H's from within the Builder module 3) Load the esff force field using select with clearing of charges and potential and making a local copy of the force field. 4) As I do not know the charge on the protein I used the Set_Charge script that initializes all charges to zero and prompts for the formal charges on the Zn atoms. I assigned +2 to each Zn when prompted. 5) From the forcefield menu I then selected potentials using fix for potentials, Accept for partial charges and Fix for formal charge. This results in an error message saying that formal charge cannot be assigned to my system. According to the manual, if this happens then one should use in this step Accept for formal charges which I did and seems to have no problems. 6) As a test, I requested a minimization. The process fails and in the output message I get the following: randomSeed is set to 618699 Line 12:BTCL> begin Error: Molecule/Monomer/Atom error in Atom-2 bonding invoked from within "begin" Total time used by DISCOVER: 1.27 secs Completion date: Thu Sep 1 16:51:40 2005 Exiting Discover: An ERROR has occurred! I would be very grateful for any help with this problem. Thanks. Maurizzio m.argonni"AT"gmail.REMOVETHIS.com P.S.: 1) Water molecules in the pdb file were taken out with the exception of HOH 935 which is the bridging water. 2) The input script created by insight is the following: BIOSYM btcl 3 Input File For Discover Generated By Insight 2000 Date: Thu Sep 1 16:51:38 2005 Host Type: iris System Name: P_1AMP Stage Name: 1 begin begin set esffCalculateCharges 0 Stage Name: 2 minimize set esffUseQuadratic 1 minimize iteration_limit = 10 set esffUseQuadratic 0 minimize \ iteration_limit = 300 movement_limit = 0.200 \ sd \ convergence = 1000.0 line_search_precision = 0.100 \ cg \ convergence = 10.0 method = polak \ line_search_precision = 0.100 \ newton \ convergence = 0.001 method = bfgs \ line_search_precision = 0.900 max_atoms = 200 \ final_convergence = 0.001 writeFile coordinate filename = .cor From owner-chemistry@ccl.net Fri Sep 2 08:20:56 2005 From: "CCL" To: CCL Subject: CCL: Automated standardization of atom names in PDB? Message-Id: <-29054-050902073126-14889-j6jGbi4IRXakbS2fcikGlA*|*server.ccl.net> X-Original-From: Dr Seth Olsen Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 02 Sep 2005 19:33:13 +0900 MIME-Version: 1.0 Sent to CCL by: Dr Seth Olsen [s.olsen1*|*uq.edu.au] Hi CCLers, Does software exist that will take a PDB format file with non-standard atom names and determine the standard atom labelling for the atoms in a file (if the file contains a protein with regular amino acid residues)? I have a PDB file that was run through a chemistry utility, and in the process the usual PDB labelling (i.e. CA, CB, HB etc.) was changed to a much less informative format. The program also modified the structure in such a way that pasting the old names in to the appropriate field is not feasible. To check all atoms would be time-consuming, but since most amino acids in the protein are unmodified, the correct atom labelling should be clear from the bond topology. Is there a program that will read the topology and determine the standard atom names? Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1*|*uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms From owner-chemistry@ccl.net Fri Sep 2 10:41:19 2005 From: "CCL" To: CCL Subject: CCL: GB+QM with mulliken charges ! Message-Id: <-29055-050902092859-9759-j6jGbi4IRXakbS2fcikGlA]^[server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-1--819440334 Date: Fri, 2 Sep 2005 07:28:51 -0500 Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: Christopher Cramer [cramer]^[chem.umn.edu] --Apple-Mail-1--819440334 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Pradipta, Mulliken charges are extraordinarily basis set dependent and tend to become highly nonphysical as one moves beyond a minimal basis representation. Since the solvation free energy is non-linear in the GB charge representation, this can lead to severe problems. That is why the SMx GB models rely on Loewdin charges (these, too, show some basis set dependence, which is one reason the CMx charge models are used to "preprocess" the Loewdin charges when we compute SMx solvation free energies). You might find the following reference (and references therein) germane: Li, J.; Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. "Universal Reaction Field Model Based on ab initio Hartree-Fock Theory" Chem. Phys. Lett. 1998, 288, 293. Best regards, Chris Cramer On Sep 2, 2005, at 4:04 AM, CCL wrote: > > Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta:+:iitg.ernet.in] > Dear All, > > I am trying to implement Generalized Born with Hartree-Fock thoery > using > mulliken charges. However, I am getting severe convergence problem. > Does > anyone have similar experience and know how to overcome that? I would > appreciate any response. > > Pradipta > > > Dr. Pradipta Bandyopadhyay > Assistant Professor > Dept. of Biotechnology > Indian Institute of Technology, Guwahati > Phone: 91-361-258-2213 (office) > e-mail: pradipta]^[iitg.ernet.in > web: http://202.141.80.5/~pradipta/Pradipta.htm > > > ----------------------------------------------------------------------- > ------------ > This email was sent from IIT Guwahati Webmail. If you are not the > intended recipient, please contact the sender by email and delete all > copies; your cooperation in this regard is appreciated. > http://www.iitg.ernet.in> 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> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (612) 597-5275 cramer]^[pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-1--819440334 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Pradipta, Mulliken charges are extraordinarily basis set dependent and tend to become highly nonphysical as one moves beyond a minimal basis representation. Since the solvation free energy is non-linear in the GB charge representation, this can lead to severe problems. That is why the SMx GB models rely on Loewdin charges (these, too, show some basis set dependence, which is one reason the CMx charge models are used to "preprocess" the Loewdin charges when we compute SMx solvation free energies). You might find the following reference (and references therein) germane: Times Li, J.; Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. "Universal Reaction Field Model Based on ab initio Hartree-Fock Theory" Chem. Phys. Lett. 1998, 288, 293. Best regards, Chris Cramer On Sep 2, 2005, at 4:04 AM, CCL wrote: Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta:+:iitg.ernet.in] Dear All, I am trying to implement Generalized Born with Hartree-Fock thoery using mulliken charges. However, I am getting severe convergence problem. Does anyone have similar experience and know how to overcome that? I would appreciate any response. Pradipta Dr. Pradipta Bandyopadhyay Assistant Professor Dept. of Biotechnology Indian Institute of Technology, Guwahati Phone: 91-361-258-2213 (office) e-mail: pradipta]^[iitg.ernet.in web: http://202.141.80.5/~pradipta/Pradipta.htm ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.in-- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (612) 597-5275 cramer]^[pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-1--819440334-- From owner-chemistry@ccl.net Fri Sep 2 13:38:23 2005 From: "CCL" To: CCL Subject: CCL: GB+QM with mulliken charges ! Message-Id: <-29056-050902125446-17254-j6jGbi4IRXakbS2fcikGlA]*[server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 02 Sep 2005 11:13:35 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel]*[attglobal.net] Chris, Just curious... PLease remind me.. do gaussian basis sets have longer tails than Slaters? If so, would using Slaters, as in ADF, make a significant difference in Mulliken and Loewdin populations? Best regards, John McKelvey PS.. already have 19 speakers for DFTB Symp for S-F. CCL wrote: > Pradipta, > > Mulliken charges are extraordinarily basis set dependent and tend to > become highly nonphysical as one moves beyond a minimal basis > representation. Since the solvation free energy is non-linear in the > GB charge representation, this can lead to severe problems. That is > why the SMx GB models rely on Loewdin charges (these, too, show some > basis set dependence, which is one reason the CMx charge models are > used to "preprocess" the Loewdin charges when we compute SMx solvation > free energies). > > You might find the following reference (and references therein) germane: > > Li, J.; Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. "Universal > Reaction Field Model Based on ab initio Hartree-Fock Theory" / Chem. > Phys. Lett./ *1998*, /288/, 293. > > Best regards, > > Chris Cramer > > On Sep 2, 2005, at 4:04 AM, CCL wrote: > > > Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta:+:iitg.ernet.in] > Dear All, > > I am trying to implement Generalized Born with Hartree-Fock thoery > using > mulliken charges. However, I am getting severe convergence > problem. Does > anyone have similar experience and know how to overcome that? I would > appreciate any response. > > Pradipta > > > Dr. Pradipta Bandyopadhyay > Assistant Professor > Dept. of Biotechnology > Indian Institute of Technology, Guwahati > Phone: 91-361-258-2213 (office) > e-mail: pradipta]*[iitg.ernet.in > web: http://202.141.80.5/~pradipta/Pradipta.htm > > > ----------------------------------------------------------------------------------- > > This email was sent from IIT Guwahati Webmail. If you are not the > intended recipient, please contact the sender by email and delete > all copies; your cooperation in this regard is appreciated. > http://www.iitg.ernet.in > > -- > > Christopher J. Cramer > University of Minnesota > Department of Chemistry > 207 Pleasant St. SE > Minneapolis, MN 55455-0431 > -------------------------- > Phone: (612) 624-0859 || FAX: (612) 626-2006 > Mobile: (612) 597-5275 > cramer]*[pollux.chem.umn.edu > http://pollux.chem.umn.edu/~cramer > (website includes information about the textbook "Essentials > of Computational Chemistry: Theories and Models, 2nd Edition") > > From owner-chemistry@ccl.net Fri Sep 2 20:13:34 2005 From: "CCL" To: CCL Subject: CCL: gamess and amd64 Message-Id: <-29057-050902184444-11047-j6jGbi4IRXakbS2fcikGlA[A]server.ccl.net> X-Original-From: Qadir Timerghazin Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 2 Sep 2005 14:52:51 -0400 Mime-Version: 1.0 Sent to CCL by: Qadir Timerghazin [qadir.timerghazin[A]gmail.com] Worked fine for me on opteron running Suse 9.1. What exactly does not work for you? Qadir On 9/1/05, CCL wrote: > > 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> > > > -- **************************************************************************** Qadir K. Timerghazin Centre for Research in Molecular Modeling (CERMM) Concordia University Richard J. Renaud Science Complex 7141 Sherbrooke St.West Montréal, Québec, CANADA H4B 1R6 Phone: (514) 848 2424 x3336 **************************************************************************** From owner-chemistry@ccl.net Fri Sep 2 20:13:34 2005 From: "CCL" To: CCL Subject: CCL: GB+QM with mulliken charges ! Message-Id: <-29058-050902182848-10126-j6jGbi4IRXakbS2fcikGlA|"|server.ccl.net> X-Original-From: "Shobe, David" content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 2 Sep 2005 14:56:40 -0400 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe|"|sud-chemieinc.com] Chris Cramer wrote: > Mulliken charges are extraordinarily basis set dependent Pradipta, Just for fun & your education, try this. Calculate LiF diatomic using a minimal basis for F and a very large basis set for Li. Observe which element has the negative Mulliken charge. :-) An extreme and perhaps silly example, but it does illustrate the basis set dependence of Mulliken charges. --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. ________________________________ > From: owner-chemistry|"|ccl.net [mailto:owner-chemistry|"|ccl.net] Sent: Friday, September 02, 2005 8:29 AM To: Shobe, David Subject: CCL: GB+QM with mulliken charges ! Pradipta, Mulliken charges are extraordinarily basis set dependent and tend to become highly nonphysical as one moves beyond a minimal basis representation. Since the solvation free energy is non-linear in the GB charge representation, this can lead to severe problems. That is why the SMx GB models rely on Loewdin charges (these, too, show some basis set dependence, which is one reason the CMx charge models are used to "preprocess" the Loewdin charges when we compute SMx solvation free energies). You might find the following reference (and references therein) germane: Li, J.; Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. "Universal Reaction Field Model Based on ab initio Hartree-Fock Theory" Chem. Phys. Lett. 1998, 288, 293. Best regards, Chris Cramer On Sep 2, 2005, at 4:04 AM, CCL wrote: Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta:+:iitg.ernet.in] Dear All, I am trying to implement Generalized Born with Hartree-Fock thoery using mulliken charges. However, I am getting severe convergence problem. Does anyone have similar experience and know how to overcome that? I would appreciate any response. Pradipta Dr. Pradipta Bandyopadhyay Assistant Professor Dept. of Biotechnology Indian Institute of Technology, Guwahati Phone: 91-361-258-2213 (office) e-mail: pradipta|"|iitg.ernet.in web: http://202.141.80.5/~pradipta/Pradipta.htm ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.in -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (612) 597-5275 cramer|"|pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition")