From owner-chemistry@ccl.net Sun Nov 23 02:37:00 2008 From: "chupvl chupvl*|*gmail.com" To: CCL Subject: CCL: failed drugs Message-Id: <-38143-081122171942-30780-3FRcnFRPqRi+DtYSc45Xhg()server.ccl.net> X-Original-From: chupvl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 23 Nov 2008 01:19:09 +0300 MIME-Version: 1.0 Sent to CCL by: chupvl [chupvl[#]gmail.com] I think there is no such kind of database, but you can look in some drug-related databases - Prous (now Thomson Reuters) - seems most comprehensive to my mind (no an ad...) - MDL Drug data report (now Symyx) - categories withdrawn and discontinued are exist - PHARMA (http://newmeds.phrma.org/0 - seems only drug in development - etc...there are a lot of drug databases from various vendors as also open access (I think) But for the most interest not the list itslef but the reason for the failure - that database will be priceless :) (eg http://bioinf.charite.de/superdrug/) Yours, Vladimir Chupakhin Moscow State University James T Metz James.Metz]_[Abbott.com wrote: > Sent to CCL by: "James T Metz" [James.Metz .. Abbott.com] > CCL, > > Does anyone maintain a well-curated list of failed drugs or failed drug candidates and when they failed e.g., Phase II, Phase III, market, etc. > > Such a list might be useful for making comparisons to drugs which did not > fail. > > Useful literature references or other sources of information would be much appreciated. > > Regards, > Jim Metz > > Abbott Laboratories> > > > From owner-chemistry@ccl.net Sun Nov 23 06:36:01 2008 From: "may abdelghani may01dz]|[yahoo.fr" To: CCL Subject: CCL: exercises resolved, for teaching Message-Id: <-38144-081123034905-19922-OzHR9xD+IVoTF4Ip2ROj2w(~)server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-727739163-1227426533=:70436" Date: Sun, 23 Nov 2008 07:48:53 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz|a|yahoo.fr] --0-727739163-1227426533=:70436 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable dear CCLers, I am a teacher of theoritical chemistry, =C2=A0and i loock for=C2=A0exercis= es resolved on the folowing subjects( if it is a possible): 1- solution of the Schrodinger equation for the hydrogen atom=20 2- Variation method 3- huckel simple thanks=0A=0A=0A --0-727739163-1227426533=:70436 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
dear CCLers,
I am a teacher of theoritical che= mistry,  and i loock for exercises resolved on the folowing subje= cts( if it is a possible):
1- solution of the Schrod= inger equation for the hydrogen atom
2- Variation method
3- huckel simple
thanks
=0A=0A=0A=0A --0-727739163-1227426533=:70436-- From owner-chemistry@ccl.net Sun Nov 23 09:53:01 2008 From: "William F. Coleman wcoleman_+_wellesley.edu" To: CCL Subject: CCL: exercises resolved, for teaching Message-Id: <-38145-081123095106-26444-qApWNNZm48zjsXS0oyPOZA=-=server.ccl.net> X-Original-From: "William F. Coleman" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Sun, 23 Nov 2008 09:50:53 -0500 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman[]wellesley.edu] "CCL Subscribers" on Sunday, November 23, 2008 at 2:48 AM -0500 wrote: >dear CCLers, >I am a teacher of theoritical chemistry,  and i loock for exercises >resolved on the folowing subjects( if it is a possible): >1- solution of the Schrodinger equation for the hydrogen atom >2- Variation method >3- huckel simple >thanks I would suggest starting with the Journal of Chemical Education. There is a web-based collection of exercises using computer algebra systems that address all areas of chemistry, including a number directed toward theoretical chemistry. Included are topics such as: Symbolic Math Approach To Solve Particle-in-the-Box and H-Atom Problems Construction of the Electronic Angular Wave Functions and Probability Distributions of the Hydrogen Atom Exploring Orthonormal Functions Exploring the Harmonic Oscillator Wave Function Components Potential Barriers and Tunneling Visualization of Wavefunctions of the Ionized Hydrogen Molecule Variational Methods Applied to the Particle in a Box and many others - these are all part of the SymMath Collection - http://jchemed.chem.wisc.edu/JCEDLib/SymMath/collection/index.php One of the features I edit for the Journal, the WebWare feature, also has some theoretical chemistry applications including: Restricted Hartree-Fock SCF Calculations Using Microsoft Excel Self-Consistent Field Calculations Spreadsheet The Effect of Anharmonicity on Diatomic Vibration: A Spreadsheet Simulation Hückel Determinant Solver These are at http://jchemed.chem.wisc.edu/JCEDLib/WebWare/collection/reviewed/index.html The print version of the Journal also contains many articles dealing with theoretical chemistry topics. All of these are part of the National Science Digital Library - http://nsdl.org/ I hope this helps, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html Editor, JCE WebWare and JCE Featured Molecules http://www.jce.divched.org/JCEDLib/WebWare/ http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html From owner-chemistry@ccl.net Sun Nov 23 12:26:01 2008 From: "Andrea Coletta andrea_coletta*_*libero.it" To: CCL Subject: CCL:G: Hessian Matrix in Internal Coordinates Message-Id: <-38146-081123121321-24429-a4md6VZ5ISxk60n0Ewg/eQ+/-server.ccl.net> X-Original-From: Andrea Coletta Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Sun, 23 Nov 2008 17:33:33 +0100 MIME-Version: 1.0 Sent to CCL by: Andrea Coletta [andrea_coletta,,libero.it] Hi, i'm trying to obtain the Hessian Matrix output in Internal Coordinates, from a B3LYP Optimization job with Gaussian03.C02. My route section is: #P B3LYP/6-31G* OPT=CalcAll SCRF=CPCM if I use this with a small molecule (e.g Water), in the log file I find something like: (Enter /apps/GEN03.C02/g03/l103.exe) GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Internal Forces: Max 0.000010959 RMS 0.000006781 Search for a local minimum. Step number 4 out of a maximum of 20 All quantities printed in internal units (Hartrees-Bohrs-Radians) Second derivative matrix not updated -- analytic derivatives used. Trust test= 1.00D+00 RLast= 3.53D-03 DXMaxT set to 4.24D-01 The second derivative matrix: R1 R2 A1 R1 0.46509 R2 -0.00302 0.46509 A1 0.02978 0.02978 0.16989 Eigenvalues --- 0.16394 0.46802 0.46812 RFO step: Lambda= 0.00000000D+00. and this is exactly what I want! It works also with an HF Opt test-job I did with Glycine: #P HF/3-21G OPT=(ModRedundant,CalcAll) SCRF=pcm [...] Force constants in Cartesian coordinates: 1 2 3 4 5 1 0.809587D+00 2 0.000000D+00 0.790299D+00 3 0.137405D-01 0.000000D+00 0.642144D+00 4 -0.114527D+00 0.000000D+00 -0.475510D-02 0.644272D+00 5 0.000000D+00 -0.110951D+00 0.000000D+00 0.000000D+00 0.621385D+00 6 0.118871D-01 0.000000D+00 -0.243725D+00 -0.379120D-02 0.000000D+00 [...] Force constants in internal coordinates: 1 2 3 4 5 1 0.426378D+00 2 0.122242D-01 0.472234D+00 3 0.115444D-01 0.547739D-02 0.471563D+00 4 0.115444D-01 0.547739D-02 0.574356D-02 0.471563D+00 5 0.138575D-01 -0.102523D-02 -0.441368D-02 -0.441368D-02 0.404944D+00 6 0.737045D-02 0.195704D-03 0.204429D-03 -0.726729D-03 0.548064D-02 This is very good... the only difference is that it does'nt specify the internal coordinate, and it wrote the Matrix just before enthering l103.exe... rather than just after entering, like in the Water calculation... When I try with another molecule a little greater (33 Atoms) it does'nt work!!, It does'nt print in the log the Hessian matrix, and in the fchk I find only the Hessian Matrix in Cartesian coordinates... I use use the same Route section, and i've tried a lot of other combinations but nothing's working! #P B3LYP/6-31G* OPT=CalcAll SCRF=CPCM or #P B3LYP/6-31G* OPT=(Redundant,CalcAll) SCRF=CPCM or #P B3LYP/6-31G* OPT=(ModRedundant,CalcAll) SCRF=CPCM or #P B3LYP/6-31G* OPT=CalcFC etc. etc. Maybe the problem is that my system has too many internal degree of freedom (96)? Any Suggestions? Please Help me!! :-( Thanks ***************************** Andrea Coletta Post-Grad. Student University of "Tor Vergata" Rome - Italy ***************************** From owner-chemistry@ccl.net Sun Nov 23 13:01:01 2008 From: "Yong Wang anhui.wangyong::gmail.com" To: CCL Subject: CCL: the ionization potentials of p-(MeO, H, Cl, NO2)-phenyl-methyl-sulfane Message-Id: <-38147-081123092126-24591-PJAWtyAU9It1tkWpbfaBHA[#]server.ccl.net> X-Original-From: "Yong Wang" Date: Sun, 23 Nov 2008 09:21:22 -0500 Sent to CCL by: "Yong Wang" [anhui.wangyong/./gmail.com] Dear CCLers, Recently, I research the mechanism of S-oxidation of a series of para- substituted sulfane derivatives: p-(MeO, H, Cl, NO2)-phenyl-S-methyl. I want know the experimental ionization potentials (IPs) of these compounds, Could anyone kindly tell me where I can find the IPs? Any responses will be greatly appreciated! Yong Wang Department of Organic Chemistry Hebrew University of Jerusalem The Hebrew University, Givat Ram Campus Jerusalem, 91904,Israel Email: wangy/./yfaat.ch.huji.ac.il or anhui.wangyong/./gmail.com From owner-chemistry@ccl.net Sun Nov 23 13:35:01 2008 From: "Sachin Tyagi sachintyagi1 * gmail.com" To: CCL Subject: CCL:G: Gaussian error/basis sets Message-Id: <-38148-081123132845-31759-1R4IqcLSQ7t8nU1vHTpwLA{:}server.ccl.net> X-Original-From: Sachin Tyagi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 23 Nov 2008 12:27:50 -0600 MIME-Version: 1.0 Sent to CCL by: Sachin Tyagi [sachintyagi1]=[gmail.com] Hi Ol Ga, Thanks for your reply, I tried the way u suggested me but I am still getting the same error General basis read from cards: (5D, 7F) WANTED AN INTEGER AS INPUT. FOUND A FLOATING POINT NUMBER AS INPUT. 1 2 1.0 5 2.0 22 1.0 ? Error termination via Lnk1e in /usr/common/g03/l301.exe If you want I can send you my input file as well. Please help, thanks in advance... Sachin Ol Ga eurisco1%x%pochta.ru wrote: > Sent to CCL by: "Ol Ga" [eurisco1_+_pochta.ru] > Dear sachin Tyagi, > > About your input : you should use keyword pseudo=read in addition of GEN. I made some threads in CCL about this subject, e.g. > http://www.ccl.net/chemistry/resources/messages/2008/07/14.004-dir/index.html > > http://www.ccl.net/cgi-bin/ccl/message-new?2008+07+14+007+raw > > and, please, dont forget to type 6d 10f (explicit definitions are more reliable) if you use 6-31G* basis set. > Obviously, you can find in CCL many other messages of CCLers with correct route cards in similar cases. > > What ECP + basis set(s) are you better to use? It is difficult to answer. But there are general suggestions: dont forget polarization functions; triple exponential basis sets are more reliable than bi-exponential basis sets; possible, ECP (small core) from Stuttgart-Dresden group in more reliable than ECP from Los-Alamos. > > Sincerely, > > Ol Ga > > > > > >> Sent to CCL by: "sachin Tyagi" [styagi2,uic.edu] >> Could any body please tell me how to assign different basis sets >> for different atoms. I read in few books and checked some sample >> input file and I tried using Keyword GEN and at the end of molecule >> specifications I assigned the basis sets, (6-31G, LanL2DZ). But I am getting the following error: >> > > >> General basis read from cards: (5D, 7F) >> WANTED AN INTEGER AS INPUT. >> FOUND A FLOATING POINT NUMBER AS INPUT. >> 1 2 1.0 5 2.0 22 1.0 >> >> >> >> ? >> Error termination via Lnk1e in /usr/common/g03/l301.exe at Fri Nov 21 >> > > >> It would be a great help if you could suggest me what basis sets >> should I be using for Iodine and transition metal atoms (Rhodium and Copper). >> > > >> Thanks >> > > >> Regards >> > > >> Sachin> > > > From owner-chemistry@ccl.net Sun Nov 23 15:32:01 2008 From: "Ol Ga eurisco1=-=pochta.ru" To: CCL Subject: CCL:G: Re2:Gaussian error/basis sets Message-Id: <-38149-081123152609-6546-wwlhmYQsWxauwntyging6Q~~server.ccl.net> X-Original-From: "Ol Ga" Date: Sun, 23 Nov 2008 15:26:05 -0500 Sent to CCL by: "Ol Ga" [eurisco1]_[pochta.ru] Dear Sachin Tyagi, I prepared special for you an example. Please, see it below. I think you were better to include your input (possible a part of your input) in your first message. Sincerely, Ol Ga For instance, # hf/gen 6D 10F NoSymm pseudo=read opt Title Card Required 0 2 Cu -1.12321078 -0.95203662 2.44003108 I 1.37678922 -0.95203662 2.44003108 C -3.06321078 -0.95203662 2.44003108 C -3.76073222 -1.87998583 3.21388218 C -3.76071639 -0.02430264 1.66650427 C -5.15544414 -1.88056468 3.21362180 H -3.21053918 -2.61175996 3.82300944 C -5.15585427 -0.02411075 1.66689774 H -3.21111910 0.70725181 1.05666828 C -5.85327558 -0.95211409 2.44017023 H -5.70530701 -2.61235963 3.82306703 H -5.70553927 0.70775084 1.05722633 C -7.39327534 -0.95296913 2.44017045 H -7.74957292 -1.61744596 1.68094546 H -7.74976084 -1.27853559 3.39506551 H -7.75049164 0.03648011 2.24450053 {blank line} 14 15 16 0 sto-3g **** 13 0 SVP **** 11 12 7 9 0 svp **** 3 4 5 6 8 10 0 TZV **** 1 0 lanl2dz **** 2 0 SVP **** {blank line} 1 0 lanl2dz > Sent to CCL by: Sachin Tyagi [sachintyagi1]=[gmail.com] > Hi Ol Ga, > Thanks for your reply, I tried the way u suggested me but I am still > getting the same error > General basis read from cards: (5D, 7F) > WANTED AN INTEGER AS INPUT. > FOUND A FLOATING POINT NUMBER AS INPUT. > 1 2 1.0 5 2.0 22 1.0 > > > > ? > Error termination via Lnk1e in /usr/common/g03/l301.exe > If you want I can send you my input file as well. Please help, thanks in advance... > Sachin > Ol Ga eurisco1%x%pochta.ru wrote: >> Sent to CCL by: "Ol Ga" [eurisco1_+_pochta.ru] >> Dear sachin Tyagi, >> >> About your input : you should use keyword pseudo=read in addition of GEN. I made some threads in CCL about this subject, e.g. >> http://www.ccl.net/chemistry/resources/messages/2008/07/14.004-dir/index.html >> >> http://www.ccl.net/cgi-bin/ccl/message-new?2008+07+14+007+raw >> >> and, please, dont forget to type 6d 10f (explicit definitions are more reliable) if you use 6-31G* basis set. >> Obviously, you can find in CCL many other messages of CCLers with correct route cards in similar cases. >> >> What ECP + basis set(s) are you better to use? It is difficult to answer. But there are general suggestions: dont forget polarization functions; triple exponential basis sets are more reliable than bi-exponential basis sets; possible, ECP (small core) from Stuttgart-Dresden group in more reliable than ECP from Los-Alamos. >> >> Sincerely, >> >> Ol Ga >> >>> Sent to CCL by: "sachin Tyagi" [styagi2,uic.edu] >>> Could any body please tell me how to assign different basis sets >>> for different atoms. I read in few books and checked some sample >>> input file and I tried using Keyword GEN and at the end of molecule >>> specifications I assigned the basis sets, (6-31G, LanL2DZ). But I am getting the following error: >>> General basis read from cards: (5D, 7F) >>> WANTED AN INTEGER AS INPUT. >>> FOUND A FLOATING POINT NUMBER AS INPUT. >>> 1 2 1.0 5 2.0 22 1.0 >>> >>> >>> >>> ? >>> Error termination via Lnk1e in /usr/common/g03/l301.exe at Fri Nov 21 >>> >> >> >>> It would be a great help if you could suggest me what basis sets >>> should I be using for Iodine and transition metal atoms (Rhodium and Copper). >>> Thanks >>> Regards >>> Sachin> From owner-chemistry@ccl.net Sun Nov 23 19:50:01 2008 From: "Anuradha Mittal amitta2++uic.edu" To: CCL Subject: CCL: build missing residues in pdb Message-Id: <-38150-081123194748-29366-0tFPSyCEWmCOfjLiq9O69g*server.ccl.net> X-Original-From: "Anuradha Mittal" Content-Type: multipart/alternative; boundary="----=_Part_145584_32255696.1227487657152" Date: Sun, 23 Nov 2008 18:47:37 -0600 MIME-Version: 1.0 Sent to CCL by: "Anuradha Mittal" [amitta2_-_uic.edu] ------=_Part_145584_32255696.1227487657152 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all, I need to simulate a protein but it is missing some residues in its pdb file. Is there any way I can add these missing residues? I tried Swiss-PdbViewer, but it doesn't seem do a great job. Even after minimization, the bonds remain grossly distorted. Any help will be much appreciated! Thanks Anu ------=_Part_145584_32255696.1227487657152 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi all,

I need to simulate a protein but it is missing some residues in its pdb file. Is there any way I can add these missing residues?
I tried Swiss-PdbViewer, but it doesn't seem do a great job. Even after minimization, the bonds remain grossly distorted.
Any help will be much appreciated!

Thanks
Anu
------=_Part_145584_32255696.1227487657152-- From owner-chemistry@ccl.net Sun Nov 23 20:43:00 2008 From: "Joe Corkery jcorkery|a|eyesopen.com" To: CCL Subject: CCL: failed drugs Message-Id: <-38151-081123163106-3658-nBkAMdlhYIDR4+1e5eSIDQ**server.ccl.net> X-Original-From: Joe Corkery Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Sun, 23 Nov 2008 13:00:40 -0800 MIME-Version: 1.0 Sent to CCL by: Joe Corkery [jcorkery() eyesopen.com] I am not aware of a single database which contains this information, but mo= st of the prominent medical journals (e.g. NEJM, JAMA, Lancet, Annals of In= ternal Medicine, etc) began requiring in 2005 that all clinical trials be r= egistered at their initiation in order for them to be considered for public= ation at a later date. www.clinicaltrials.gov was referenced back in the or= iginal article as being the only registry at that time (2004) which met the= ir criteria. This site is relatively new (i.e. will only have data from thi= s decade) but going forward this could be a valuable resource. From the fol= low up article in these journals regarding trial registration (2007) it sta= ted that an additional four registries were created or became compliant sin= ce the original publication that met their criteria (sadly, they don't list= these registries). One of these might be the WHO registry which can be fou= nd at: http://www.who.int/ictrp/en/. If you go to either of the sites and simply search for the terms terminated= or withdrawn it gives you a long list of studies which can be viewed. You = can pair these terms with therapeutic areas as well for more detailed searc= hes. With regards to approved drugs, the FDA reported a list of drugs withdrawn = up to 2005 in the following document: http://www.fda.gov/CDER/reports/rtn/2005/rtn2005-4.htm And active post-market studies can be found here: http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfPMA/pma_pas.cfm Hopefully, you will be able to find some or all of these sites useful. Best= of luck, Joe Corkery OpenEye Scientific Software -----Original Message----- > From: owner-chemistry+jcorkery=3D=3Deyesopen.com[a]ccl.net [mailto:owner-chem= istry+jcorkery=3D=3Deyesopen.com[a]ccl.net] On Behalf Of James T Metz James.M= etz]_[Abbott.com Sent: Friday, November 21, 2008 5:00 PM To: Joe Corkery Subject: CCL: failed drugs Sent to CCL by: "James T Metz" [James.Metz .. Abbott.com] CCL, Does anyone maintain a well-curated list of failed drugs or failed drug can= didates and when they failed e.g., Phase II, Phase III, market, etc. Such a list might be useful for making comparisons to drugs which did not fail. Useful literature references or other sources of information would be much = appreciated. Regards, Jim Metz Abbott Laboratories -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt