From owner-chemistry@ccl.net Mon Jun 15 07:40:01 2009 From: "Bikadi Zsolt zsolt.bikadi(_)virtuadrug.com" To: CCL Subject: CCL: How to select protien for docking Message-Id: <-39511-090615065258-30564-xMFnDSYB5PWkSHn8UzDnNw(!)server.ccl.net> X-Original-From: "Bikadi Zsolt" Content-Language: hu Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 15 Jun 2009 08:44:36 +0200 MIME-Version: 1.0 Sent to CCL by: "Bikadi Zsolt" [zsolt.bikadi|virtuadrug.com] Hello, I would recommend DockingServer (http://www.dockingserver.com) for you, which is an easy to use docking server based on Autodock and MOPAC. You can search for protein structures there. If your target protein has numerous X-ray structures, the best you can do is to dock to each different ligand bound structure. Yo do don need top re-fit the ligand into the binding site, only select a region or the whole protein for docking. Zsolt -----Original Message----- > From: owner-chemistry+zsolt.bikadi==virtuadrug.com^-^ccl.net [mailto:owner-chemistry+zsolt.bikadi==virtuadrug.com^-^ccl.net] On Behalf Of james peter jp07:+:sify.com Sent: Sunday, June 14, 2009 2:14 PM To: Bikadi, Zsolt Subject: CCL: How to select protien for docking Sent to CCL by: "james peter" [jp07,sify.com] Hi, My work is on synthetic chemistry. I have synthesized a series of biologically activ compounds. just I want to perform protien ligand docking taking my molecules as ligand. My problem is how can I select a protien and > from where I can download a protien. I have read many tutorials describing method of docking taking an example protien and ligand. but my problem is how to select a protien from a wide list of protien structures and how to fit ligand structure into protine for docking. Please help me so that I can perform docking. Thanking in advance J.Peterhttp://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 Mon Jun 15 08:14:00 2009 From: "Paul Wilhelm Elsinghorst paul]=[uni-bonn.de" To: CCL Subject: CCL:G: conformational analysis, distribution from relaxed PES scan Message-Id: <-39512-090615053724-7091-6rBfkp2BdCzEAA8riZFAJQ^server.ccl.net> X-Original-From: Paul Wilhelm Elsinghorst Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Mon, 15 Jun 2009 07:40:56 +0200 Mime-Version: 1.0 Sent to CCL by: Paul Wilhelm Elsinghorst [paul _ uni-bonn.de] Hi, I need some help with Gaussian03. How can I calculate the distribution for all minima obtained from a relaxed PES scan? I need something like: minimum1 4% minimum2 25% minimum3 35% minimum4 1% Thanks in advance, Paul From owner-chemistry@ccl.net Mon Jun 15 08:49:00 2009 From: "Suyambu Keasava Vijayan vijayan_rs(_)iicb.res.in" To: CCL Subject: CCL: Ensemble aveaging of XRD structures Message-Id: <-39513-090615070840-488-Rvzsb2Isti43yk1KUovmsA%%server.ccl.net> X-Original-From: "Suyambu Keasava Vijayan" Date: Mon, 15 Jun 2009 07:08:36 -0400 Sent to CCL by: "Suyambu Keasava Vijayan" [vijayan_rs a iicb.res.in] Dear CCL members I have 10 crystal structures for a protein, and i want to get an ensemble averaged structure for the same. Can it be performed using GROMACS or VMD, because ensemble averaging is done usually for MD trajectories using these softwares. Unfortunately I also found that each crystal structures have different missing residues, hence performing averaging using the g_rmsf command in gromacs also failed. Anticipating replies from CCL members and thanking in advance Regards Vijayan.R Senior Research Fellow Structural Biology & Bioinformatics Division Indian Institute of Chemical Biology Kolkata India From owner-chemistry@ccl.net Mon Jun 15 09:27:01 2009 From: "partha kundu partha1kundu(0)yahoo.com" To: CCL Subject: CCL:G: percentage distribution of the potential energy Message-Id: <-39514-090615043607-323-dV52eDtOJryM05l2RRF0Xw###server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary="0-2016349297-1245048555=:74125" Date: Sun, 14 Jun 2009 23:49:15 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu ~~ yahoo.com] --0-2016349297-1245048555=:74125 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable This is not possible in Gaussian 03. I am also trying to do the same thing.= It may be possible in gamess but I could not do it. --- On Sun, 6/14/09, salah said m-22*_*hotmail.fr = wrote: > From: salah said m-22*_*hotmail.fr Subject: CCL:G: percentage distribution of the potential energy To: "Kundu, Partha Pratim " Date: Sunday, June 14, 2009, 4:21 PM Sent to CCL by: "salah=A0=A0=A0said" [m-22.*_*.hotmail.fr] Hi, How to calculate with gaussian03 the percentage distribution of the potenti= al energy in terms of normal modes of vibration??? Thanks. -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-2016349297-1245048555=:74125 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
This is not possible in Gaussian 03. I am als= o trying to do the same thing. It may be possible in gamess but I could not= do it.

--- On Sun, 6/14/09, salah said m-22*_*hotmail.fr <= owner-chemistry*_*ccl.net> wrote:

From: salah said m-22*_*hotmail.fr <owner-chem= istry*_*ccl.net>
Subject: CCL:G: percentage distribution of the potenti= al energy
To: "Kundu, Partha Pratim " <partha1kundu*_*yahoo.com= >
Date: Sunday, June 14, 2009, 4:21 PM


Sent to CCL by: "salah   said" [<= A href=3D"http://us.mc05g.mail.yahoo.com/mc/compose?to=3Dm-22.*_*.hotmail.fr"= ymailto=3D"mailto:m-22.*_*.hotmail.fr">m-22.*_*.hotmail.fr]
Hi,
How = to calculate with gaussian03 the percentage distribution of the potential e= nergy in terms of normal modes of vibration???
Thanks.



-= =3D This is automatically added to each message by the mailing script =3D-<= BR= l= ook up the X-Original-From: line in the mail header.

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=0A=0A = --0-2016349297-1245048555=:74125-- From owner-chemistry@ccl.net Mon Jun 15 09:59:01 2009 From: "laura S slaurami++yahoo.com" To: CCL Subject: CCL: How to select protein for docking Message-Id: <-39515-090615053310-6500-vOmPpP6GxNqDAzwcAwuqhw ~~ server.ccl.net> X-Original-From: laura S Content-Type: multipart/alternative; boundary="0-1780598090-1245048376=:52092" Date: Sun, 14 Jun 2009 23:46:16 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: laura S [slaurami:+:yahoo.com] --0-1780598090-1245048376=:52092 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Peter,=0A=0AI understood that you want to ckeck with docking how your li= gands work in some proteins (inhibitor, substrate, inert). (It's not enogh.= You have to read about every protein to know them deeply). You should chec= k the Protein Data Bank (PDB) http://www.rcsb.org/pdb/home/home.do to downl= oad X-ray structures of different proteins and you can select a protein for= docking taking into acount the active part of the protein (reading publica= tions about that protein). But here I want to mention that in some cases th= e structure are not complete for docking. For example the ammonia-lyase str= uctures have tetramer form, but in the PDB you can find them as dimer or tw= o different dimer form. From here, after you know the real form of your pro= tein and if this doesn't have the real form in the PDB you may build the re= al form in SwissPDBViewer program http://spdbv.vital-it.ch/. It depends = on your ligands too how they will fit in the protein structure. You should= check the electrophilic or nucleophilic properties at the ligands and in the act= ive part (catalitic site) of the protein. =0AFor docking you can use AutoDo= ck http://autodock.scripps.edu/, FlexX http://www.biosolveit.de/flexx/ or o= ther programs. =0AHope this helps,=0AGood work,=0AAmalia=0A=0A =0AAmalia-La= ura Seff =0A------------------------------------------------=0APhD student= =0ABabes-Bolyai University=0A=0AFaculty of Chemistry and Chemical Engineeri= ng =0AInorganic Chemistry Department=0AMolecular Modeling Laboratory 101=0A= =0AAdress: Arany J=E1nos Str. no. 11=0A Ro - 400028, Cluj-Napoc= a=0Atel: 40-264-593833/5772=0A 40-724752988=0A 36-702260428=0Afax= : 40-264-590818=0A =0A=0A=0A=0A=0A________________________________=0AFrom: = james peter jp07:+:sify.com =0ATo: "Seff, Amalia L= aura " =0ASent: Sunday, June 14, 2009 3:14:11 P= M=0ASubject: CCL: How to select protien for docking=0A=0A=0ASent to CCL by:= "james peter" [jp07,sify.com]=0AHi,=0AMy work is on synthetic chemistry. = I have synthesized a series of biologically activ compounds. just I want to= perform protien ligand docking taking my molecules as ligand. My problem i= s how can I select a protien and from where I can download a protien.=0AI h= ave read many tutorials describing method of docking taking an example prot= ien and ligand. but my problem is how to select a protien from a wide list = of protien structures and how to fit ligand structure into protine for dock= ing. Please help me so that I can perform docking.=0AThanking in advance = =0AJ.Peter=0A=0A=0A=0A-=3D This is automatically added to each message by t= he mailing script =3D-=0ATo recover the email address of the author of the = message, please change=0Athe strange characters on the top line to the [-] si= gn. You can also=0A=0A= =0A=0A http://www.ccl.= net/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-R= EQUEST[-]ccl.net or use=0A http://www.ccl.net/cgi-bin/ccl/send_ccl_messa= ge=0A=0A=0A http://www.ccl.net/chemistry/sub_un= sub.shtml=0A=0A=0A=0A==0AConferences: http://server.ccl.net/chemistr= y/announcements/conferences/=0A=0ASearch Messages: http://www.ccl.net/chemi= stry/searchccl/index.shtml=0A=0AIf your mail bounces from CCL with 5.7.1 er= ror, check:=0A=0A=0ARTFI: http://www.c= cl.net/chemistry/aboutccl/instructions/=0A=0A=0A --0-1780598090-1245048376=:52092 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Peter,

I understood that you want to ckeck wit= h docking how your ligands work in some proteins (inhibitor, substrate, ine= rt). (It's not enogh. You have to read about every protein to know them dee= ply). You should check the Protein Data Bank (PDB) http://www.rcsb.org/pdb/home/hom= e.do to download X-ray structures of different proteins and you can sel= ect a protein for docking taking into acount the active part of the protein= (reading publications about that protein). But here I want to mention that= in some cases the structure are not complete for docking. For example the = ammonia-lyase structures have tetramer form, but in the PDB you can find th= em as dimer or two different dimer form. From here, after you know the real form of your protein and if this doesn't have the real form in the PDB you= may build the real form in SwissPDBViewer program http://spdbv.vital-it.ch/.   = It depends on your ligands too how they will fit  in the protein stru= cture. You should check the electrophilic or nucleophilic properties at the= ligands and in the active part (catalitic site) of the protein. For docking you can use AutoDock http://autodock.scripps.edu/, FlexX http://www.biosolveit.= de/flexx/ or other programs.
Hope this helps,
Good work,<= br>Amalia
 
Amalia-Laura Seff <= br>------------------------------------------------
PhD student
B= abes-Bolyai University
Fa= culty of Chemistry and Chemical Engineering
Inorganic Chemistry Department
Molecular Modeling Laboratory 101
 
Adress: Arany J=E1nos Str. no= . 11
         &nbs= p;  Ro - 400028, Cluj-Napoca
tel: 40-264-593833/577= 2
      40-724752988
=       36-702260428
fax:&nb= sp;40-264-590818
 


From:= james peter jp07:+:sify.com <owner-chemistry[-]ccl.net>
= To: "Seff, Amalia Laura -i= d#3td-" <slaurami[-]yahoo.com>
Sent: Sunday, June 14, 2009 3:14:11 PM
Subject: CCL: How to select protien for docking=

=0A
Sent to CCL by: "james  peter" [jp07,sify.com]
Hi,
My work is on = synthetic chemistry. I have synthesized a series of biologically activ comp= ounds. just I want to perform protien ligand docking taking my molecules as= ligand. My problem is how can I select a protien and from where I can down= load a protien.
I have read many tutorials describing method of docking = taking an example protien and ligand. but my problem is how to select a pro= tien from a wide list of protien structures and how to fit ligand structure= into protine for docking. Please help me so that I can perform docking.Thanking in advance
J.Peter



-=3D This is automatically = added to each message by the mailing script =3D-
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=0A=0A= =0A=0A --0-1780598090-1245048376=:52092-- From owner-chemistry@ccl.net Mon Jun 15 10:34:02 2009 From: "Jamel MESLAMANI meslamani**ulp.u-strasbg.fr" To: CCL Subject: CCL: How to select protien for =?UTF-8?B?ZG9ja2luZ+KAjw==?= Message-Id: <-39516-090615052517-5651-zUfUj5h9O5ZahE99Nz7NbA,,server.ccl.net> X-Original-From: Jamel MESLAMANI Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 15 Jun 2009 10:42:26 +0200 MIME-Version: 1.0 Sent to CCL by: Jamel MESLAMANI [meslamani*o*ulp.u-strasbg.fr] Dear James, You can download protein files from the Protein Data Bank, Or from the screening PDB (sc-PDB) which is a database of druggable binding sites of the PDB. http://bioinfo-pharma.u-strasbg.fr/scPDB You can download protein file in tripos mol2 format or pdb format. You can also download the entire sc-PDB database via the ftp link available from the website. cf: Kellenberger et al. J.Chem.Inf.Model.,2008,48(5),1014-1025. DOI:10.1021/ci800023x Best Regards, Jamel. --- Sent to CCL by: "james peter" [jp07,sify.com] Hi, My work is on synthetic chemistry. I have synthesized a series of biologically activ compounds. just I want to perform protien ligand docking taking my molecules as ligand. My problem is how can I select a protien and from where I can download a protien. I have read many tutorials describing method of docking taking an example protien and ligand. but my problem is how to select a protien > from a wide list of protien structures and how to fit ligand structure into protine for docking. Please help me so that I can perform docking. Thanking in advance J.Peter From owner-chemistry@ccl.net Mon Jun 15 11:11:01 2009 From: "Michel Petitjean petitjean.chiral^-^gmail.com" To: CCL Subject: CCL: Ensemble aveaging of XRD structures Message-Id: <-39517-090615104510-24313-wWkWeZORACMkKWilqg8T0g|a|server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 15 Jun 2009 16:36:31 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral::gmail.com] Hi, Computing mean conformers or mean molecules can be done with the method described in appendix 2 of our paper in J. Chem. Inf. Model. 2009, 49(2), 330-337. You need to compute the symmetric array 10*10 of distances between your 10 structures (can be done with the ARMS freeware, which returns the RMS distance between two structures), then you compute the mean point as indicated in the paper. The result will be the structure computed as being the mean one among the 10 input ones. The method works with other distances or dissimilarities, and it works for sets of molecules with different numbers of atoms. In this case, use the freeware CSR rather than ARMS, and retain for example dist(1,2)=n1+n2-2*n12, where n12 is the number of atoms of the common 3D motif returned by CSR. The cited freewares are on my website. I never experienced the computation of mean molecules in the case of proteins: please let me know if the method above is useful in this case. Thanks. Michel Petitjean, CEA/DSV/iBiTec-S/SB2SM (CNRS URA 2096), 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean^^cea.fr, petitjean.chiral^^gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Sent to CCL by: "Suyambu Keasava Vijayan" [vijayan_rs a iicb.res.in] Dear CCL members I have 10 crystal structures for a protein, and i want to get an ensemble averaged structure for the same. Can it be performed using GROMACS or VMD, because ensemble averaging is done usually for MD trajectories using these softwares. Unfortunately I also found that each crystal structures have different missing residues, hence performing averaging using the g_rmsf command in gromacs also failed. Anticipating replies from CCL members and thanking in advance Regards Vijayan.R Senior Research Fellow Structural Biology & Bioinformatics Division Indian Institute of Chemical Biology Kolkata India From owner-chemistry@ccl.net Mon Jun 15 11:44:00 2009 From: "Shahar Keinan skeinan*_*gmail.com" To: CCL Subject: CCL: Question about GAMESS/TINKER - no link atoms Message-Id: <-39518-090615105057-28964-GYEzD94zrQ6QUxQqPA3vZg^server.ccl.net> X-Original-From: "Shahar Keinan" Date: Mon, 15 Jun 2009 10:50:53 -0400 Sent to CCL by: "Shahar Keinan" [skeinan^gmail.com] Dear all, I have submitted this question about a week ago, and have not heard anything back. I have also submitted this question to the GAMESS forum, with no reply. I am trying again. I am trying to do a QM/MM calculation with GAMESS/TINKER, however, I want to run the calculations without link atoms. Is this possible? The example files all have link atoms in them. Thank you, Dr. Shahar Keinan Duke University I am attaching an example of an input file that gets an error message (this is a water dimer, one water molecule QM, the other TIP3): ! An example file to perform ! QM/MM. ! water dimer, no link atoms. One water is TIP3, ! other water described with HF/STO-3G ! $CONTRL SCFTYP=RHF RUNTYP=optimize COORD=UNIQUE NZVAR=33 $END $BASIS GBASIS=sto NGAUSS=3 $END $ZMAT DLC=.T. AUTO=.T. $END $DATA Ab initio atoms in QM region C1 O 8.0 -0.032947 0.000000 0.005966 H 1.0 0.270601 0.000000 0.911928 H 1.0 0.792970 0.000000 -0.510216 $END $LINK IMOMM=.T. IQMATM(1)=1,2,3 $END $TINKEY parameters /home/skeinan/gamess_tinker/tinker/params/charmm $END $TINXYZ 6 water dimer 1 OT -0.032947 0.000000 0.005966 91 2 3 2 HT 0.270601 0.000000 0.911928 83 1 3 HT 0.792970 0.000000 -0.510216 83 1 4 HT 2.756636 0.756897 -1.740089 83 5 5 OT 2.373120 0.000000 -1.290448 91 4 6 6 HT 2.756636 -0.756897 -1.740089 83 5 $END From owner-chemistry@ccl.net Mon Jun 15 12:19:01 2009 From: "Manish Sud msud]_[san.rr.com" To: CCL Subject: CCL: New release of MayaChemTools package Message-Id: <-39519-090615113354-1408-zgnCPK5oXeBrT8x/ROY91w]_[server.ccl.net> X-Original-From: "Manish Sud" Date: Mon, 15 Jun 2009 11:33:50 -0400 Sent to CCL by: "Manish Sud" [msud ~ san.rr.com] The new release of MayaChemTools, a growing collection of Perl scripts and modules/classes to support day-to-day computational discovery needs, is available as free software; you can redistribute it and/or modify it under the terms of the GNU LGPL. The new scripts are: o AtomNeighborhoodsFingerprints.pl o ExtendedConnectivityFingerprints.pl o MACCSKeysFingerprints.pl o TopologicalAtomPairsFingerprints.pl o TopologicalAtomTorsionsFingerprints.pl o TopologicalPharmacophoreAtomPairsFingerprints.pl o TopologicalPharmacophoreAtomTripletsFingerprints.pl The existing scripts with new functionality are: o PathLengthFingerprints.pl o SimilarityMatrixSDFiles.pl o SimilarityMatrixTextFiles.pl o InfoFingerprintsTextFiles.pl o InfoFingerprintsSDFiles.pl The new modules/classes available for custom development are: Matrix.pm, GraphMatrix.pm, AtomicInvariantsAtomTypes.pm, FingerprintsStringUtil.pm, FingerprintsVector.pm, ExtendedConnectivityFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm, and so on. To learn more about the new functionality and download the package, please visit: www.MayaChemTools.org. Those of you who might be wondering: Where are the scripts to perform similarity searching? Well, stay tuned. Ive got a few more fingerprints on the list I would like to implement before developing scripts for similarity searching. In the mean time, please try out the new functionality and dont hesitate to send your feedback. Its very much appreciated. Happy fingerprinting. Manish Sud msud^san.rr.com From owner-chemistry@ccl.net Mon Jun 15 12:54:01 2009 From: "S. Bill S_Bill36=yahoo.co.uk" To: CCL Subject: CCL: pKa data base... Message-Id: <-39520-090615120113-24964-9RcC0W859CjylMy+pE63nw#,#server.ccl.net> X-Original-From: "S. Bill" Date: Mon, 15 Jun 2009 12:01:09 -0400 Sent to CCL by: "S. Bill" [S_Bill36]|[yahoo.co.uk] Dear CCL I was wondering if there is a data base for pKa values for ligands. Also, I found there are many papers deal with calculation of pKa values of ligands, could you recommend one for me, please? Thanks in Advance From owner-chemistry@ccl.net Mon Jun 15 13:33:00 2009 From: "neeraj misra neerajmisra-$-hotmail.com" To: CCL Subject: CCL: software Message-Id: <-39521-090615122953-17058-SlGYGGzN40/oWCtOOtG77g||server.ccl.net> X-Original-From: "neeraj misra" Date: Mon, 15 Jun 2009 12:29:49 -0400 Sent to CCL by: "neeraj misra" [neerajmisra|-|hotmail.com] IS THERE ANY WAY OUT TO MODEL DIMER, TRIMER ETC AND EVENTUALLY A CLUSTER OF AN ATOM BY A SOFTWARE PACKAGE? From owner-chemistry@ccl.net Mon Jun 15 14:04:00 2009 From: "Iain Wallace iain.m.wallace^-^gmail.com" To: CCL Subject: CCL: Free Database of Natural Products? Message-Id: <-39522-090615125529-5370-E/2kdxRdWHyZwKi/UaeVRg#%#server.ccl.net> X-Original-From: Iain Wallace Content-Type: multipart/alternative; boundary=000e0cd487d2619ff4046c65ec98 Date: Mon, 15 Jun 2009 12:55:00 -0400 MIME-Version: 1.0 Sent to CCL by: Iain Wallace [iain.m.wallace~~gmail.com] --000e0cd487d2619ff4046c65ec98 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi All, I was wondering if anybody knows of a free (or really really cheap) database of natural products? We are trying to look at properties of synthetic compounds vs. natural products. All the work in this area seems to use closed source databases like CRC Dictionary of Natural Products. Cheers, Iain --000e0cd487d2619ff4046c65ec98 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All,

I was wondering if anybody knows of a free (or really really= cheap) database of natural products? We are trying to look at properties o= f synthetic compounds vs. natural products. All the work in this area seems= to use closed source databases like CRC Dictionary of Natural Products.
Cheers,

Iain
--000e0cd487d2619ff4046c65ec98-- From owner-chemistry@ccl.net Mon Jun 15 14:40:00 2009 From: "Jose Alberto Fernandes jafernandes|-|ua.pt" To: CCL Subject: CCL:G: Calculations with PBC in Gaussian Message-Id: <-39523-090615123004-17218-YtojAK7F0qQud68CROfmnw]~[server.ccl.net> X-Original-From: "Jose Alberto Fernandes" Date: Mon, 15 Jun 2009 12:30:00 -0400 Sent to CCL by: "Jose Alberto Fernandes" [jafernandes],[ua.pt] I need to calculate vibrational data for large periodic systems. If I try to use PBC in Gaussian03 it takes too long, even for graphite which has only two atoms. Some of you know what is the problem with Gaussian, and how can I turn it faster? Jos From owner-chemistry@ccl.net Mon Jun 15 15:18:00 2009 From: "Yutao Yue yutao.yue%gmail.com" To: CCL Subject: CCL: pKa data base... Message-Id: <-39524-090615135128-17782-gMJ4SwB2nBbgmQXD9fisEQ---server.ccl.net> X-Original-From: Yutao Yue Content-Transfer-Encoding: base64 Content-Type: text/plain; charset="gb2312" Date: Mon, 15 Jun 2009 13:51:10 -0400 MIME-Version: 1.0 Sent to CCL by: Yutao Yue [yutao.yue+*+gmail.com] SSBoYXZlIGJlZW4gcmVhZGluZyBzb21lIHJlbGF0ZWQgc3R1ZmYgcmVjZW50bHksIGhlcmUgaXMg YSBuaWNlIHJldmlldzoNCg0KQW5hbHl6aW5nIGVuenltYXRpYyBwSCBhY3Rpdml0eSBwcm9maWxl cyBhbmQgcHJvdGVpbiB0aXRyYXRpb24gY3VydmVzIHVzaW5nIHN0cnVjdHVyZS1iYXNlZCBwS2Eg Y2FsY3VsYXRpb25zIGFuZCB0aXRyYXRpb24gY3VydmUgZml0dGluZywgTmllbHNlbiBKRSwgTWV0 aG9kcyBFbnp5bW9sLiAyMDA5OzQ1NDoyMzMtNTh0aGUgUHViTWVkIGxpbms6DQpodHRwOi8vd3d3 Lm5jYmkubmxtLm5paC5nb3YvcHVibWVkLzE5MjE2OTI5DQoNCkl0IHJlZmVycyB0byBtYW55IHZl cnkgdXNlZnVsIHJlZmVyZW5jZXMsIGluY2x1ZGluZyBhIHBhcGVyIGJ5IEJhc2hmb3JkLCBELiBh bmQgS2FycGx1cywgTS4gKDE5OTApLCBhbmQgYSBmZXcgZm9sbG93IHVwIHBhcGVycy4NCg0KSG9w ZSBpdCBoZWxwcy4NCg0KWXV0YW8NCg0KLS0tLS0gT3JpZ2luYWwgTWVzc2FnZSAtLS0tLSANCkZy b206ICJTLiBCaWxsIFNfQmlsbDM2PXlhaG9vLmNvLnVrIiA8b3duZXItY2hlbWlzdHJ5QGNjbC5u ZXQ+DQpUbzogIll1ZSwgWXV0YW8gLWlkIzN2Yy0iIDx5dXRhby55dWVAZ21haWwuY29tPg0KU2Vu dDogTW9uZGF5LCBKdW5lIDE1LCAyMDA5IDEyOjAxIFBNDQpTdWJqZWN0OiBDQ0w6IHBLYSBkYXRh IGJhc2UuLi4NCg0KDQo+IA0KPiBTZW50IHRvIENDTCBieTogIlMuICBCaWxsIiBbU19CaWxsMzZd fFt5YWhvby5jby51a10NCj4gRGVhciBDQ0wNCj4gSSB3YXMgd29uZGVyaW5nIGlmIHRoZXJlIGlz IGEgZGF0YSBiYXNlIGZvciBwS2EgdmFsdWVzIGZvciBsaWdhbmRzLg0KPiBBbHNvLCBJIGZvdW5k IHRoZXJlIGFyZSBtYW55IHBhcGVycyBkZWFsIHdpdGggY2FsY3VsYXRpb24gb2YgcEthIHZhbHVl cyBvZiBsaWdhbmRzLCBjb3VsZCB5b3UgcmVjb21tZW5kIG9uZSBmb3IgbWUsIHBsZWFzZT8NCj4g VGhhbmtzIGluIEFkdmFuY2UNCj4gDQo+IA0KPiANCj4gLT0gVGhpcyBpcyBhdXRvbWF0aWNhbGx5 IGFkZGVkIHRvIGVhY2ggbWVzc2FnZSBieSB0aGUgbWFpbGluZyBzY3JpcHQgPS0NCj4gVG8gcmVj b3ZlciB0aGUgZW1haWwgYWRkcmVzcyBvZiB0aGUgYXV0aG9yIG9mIHRoZSBtZXNzYWdlLCBwbGVh c2UgY2hhbmdlDQo+IHRoZSBzdHJhbmdlIGNoYXJhY3RlcnMgb24gdGhlIHRvcCBsaW5lIHRvIHRo ZSBAIHNpZ24uIFlvdSBjYW4gYWxzbw0KPiBsb29rIHVwIHRoZSBYLU9yaWdpbmFsLUZyb206IGxp bmUgaW4gdGhlIG1haWwgaGVhZGVyLg0KPiANCj4gRS1tYWlsIHRvIHN1YnNjcmliZXJzOiBDSEVN SVNUUllAY2NsLm5ldCBvciB1c2U6DQo+ICAgICAgaHR0cDovL3d3dy5jY2wubmV0L2NnaS1iaW4v Y2NsL3NlbmRfY2NsX21lc3NhZ2UNCj4gDQo+IEUtbWFpbCB0byBhZG1pbmlzdHJhdG9yczogQ0hF TUlTVFJZLVJFUVVFU1RAY2NsLm5ldCBvciB1c2UNCj4gICAgICBodHRwOi8vd3d3LmNjbC5uZXQv Y2dpLWJpbi9jY2wvc2VuZF9jY2xfbWVzc2FnZQ0KPiANCj4gU3Vic2NyaWJlL1Vuc3Vic2NyaWJl OiANCj4gICAgICBodHRwOi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L3N1Yl91bnN1Yi5zaHRtbA0K PiANCj4gQmVmb3JlIHBvc3RpbmcsIGNoZWNrIHdhaXQgdGltZSBhdDogaHR0cDovL3d3dy5jY2wu bmV0DQo+IA0KPiBKb2I6IGh0dHA6Ly93d3cuY2NsLm5ldC9qb2JzIA0KPiBDb25mZXJlbmNlczog aHR0cDovL3NlcnZlci5jY2wubmV0L2NoZW1pc3RyeS9hbm5vdW5jZW1lbnRzL2NvbmZlcmVuY2Vz Lw0KPiANCj4gU2VhcmNoIE1lc3NhZ2VzOiBodHRwOi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L3Nl YXJjaGNjbC9pbmRleC5zaHRtbA0KPiANCj4gSWYgeW91ciBtYWlsIGJvdW5jZXMgZnJvbSBDQ0wg d2l0aCA1LjcuMSBlcnJvciwgY2hlY2s6DQo+ICAgICAgaHR0cDovL3d3dy5jY2wubmV0L3NwYW1t ZXJzLnR4dA0KPiANCj4gUlRGSTogaHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9hYm91dGNj bC9pbnN0cnVjdGlvbnMvDQo+IA0KPg== From owner-chemistry@ccl.net Mon Jun 15 16:19:00 2009 From: "Josef Scheiber mail- -josef-scheiber.de" To: CCL Subject: CCL: Free Database of Natural Products? Message-Id: <-39525-090615155631-20985-6Au8wRZJ2JMw28PDk551OQ]^[server.ccl.net> X-Original-From: Josef Scheiber Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 15 Jun 2009 21:10:53 +0200 MIME-Version: 1.0 Sent to CCL by: Josef Scheiber [mail[]josef-scheiber.de] Hi Iain, check out SuperNatural: http://bioinformatics.charite.de/supernatural/ Cheers, Sepp Iain Wallace iain.m.wallace^-^gmail.com wrote: > Hi All, > > I was wondering if anybody knows of a free (or really really cheap) > database of natural products? We are trying to look at properties of > synthetic compounds vs. natural products. All the work in this area > seems to use closed source databases like CRC Dictionary of Natural > Products. > > Cheers, > > Iain From owner-chemistry@ccl.net Mon Jun 15 18:20:01 2009 From: "Esteban Gabriel Vega Hissi egvega_+_gmail.com" To: CCL Subject: CCL: pKa data base... Message-Id: <-39526-090615145955-12331-PQFb5la+pQw498Z44gXhmg{:}server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=0016364d2597505706046c67a9e9 Date: Mon, 15 Jun 2009 14:59:44 -0400 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega#,#gmail.com] --0016364d2597505706046c67a9e9 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Read Shields and Liptak papers. 2009/6/15 S. Bill S_Bill36=yahoo.co.uk > > Sent to CCL by: "S. Bill" [S_Bill36]|[yahoo.co.uk] > Dear CCL > I was wondering if there is a data base for pKa values for ligands. > Also, I found there are many papers deal with calculation of pKa values of > ligands, could you recommend one for me, please? > Thanks in Advance> > > --0016364d2597505706046c67a9e9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Read Shields and Liptak papers.


2009/= 6/15 S. Bill S_Bill36=3Dyahoo.co.uk <owner-chemistr= y::ccl.net>

Sent to CCL by: "S. =A0Bill" [S_Bill36]|[yahoo.co.uk]
Dear CCL
I was wondering if there is a data base for pKa values for ligands.
Also, I found there are many papers deal with calculation of pKa values of = ligands, could you recommend one for me, please?
Thanks in Advance



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