From owner-chemistry@ccl.net Wed Jul 11 01:21:00 2007 From: "Dan Maftei dan.maftei]![chem.uaic.ro" To: CCL Subject: CCL:G: Visualizing vibrational data Message-Id: <-34718-070710112242-7429-2JdGlvhphhFByyZDIPJH4g|server.ccl.net> X-Original-From: Dan Maftei Content-Type: multipart/mixed; boundary="------------090805090503040201020206" Date: Tue, 10 Jul 2007 16:50:20 +0300 MIME-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei~~chem.uaic.ro] This is a multi-part message in MIME format. --------------090805090503040201020206 Content-Type: text/plain; charset=ISO-8859-2; format=flowed Content-Transfer-Encoding: 7bit Jmol (http://jmol.sourceforge.net/demo/vibration/) reads and animates the calculated vibrational data directly from Gaussian frequency outputs. Don't know if it does QChem too. Soren Eustis soren(_)jhu.edu wrote: > Sent to CCL by: "Soren Eustis" [soren(~)jhu.edu] > ChemCraft is a wonderful visualization program for this purpose. > www.chemcraftprog.com > > -----Original Message----- >> From: owner-chemistry]![ccl.net [mailto:owner-chemistry]![ccl.net] > Sent: Monday, July 09, 2007 1:50 PM > To: Eustis, Soren > Subject: CCL: Visualizing vibrational data > > > Sent to CCL by: "Raoul E Correa" [raoul+*+berkeley.edu] > Hello, > > I was wondering if there is software which helps one visualize the motions > of atoms along a vibrational mode, such as those described by a frequency > calculation in any computational package. I run simulations on QChem but > haven't found a program that will take the output and create animations of > the actual vibrational mode. > > Does anyone know of such a stand-alone program? Or maybe a way to convert > the output into something that another program (e.g. Molekel) could use? > Thanks for the help! > > Raoulhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > > --------------090805090503040201020206 Content-Type: text/x-vcard; charset=utf-8; name="dan.maftei.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="dan.maftei.vcf" begin:vcard fn:Dan Maftei n:Maftei;Dan org:"Alexandru Ioan Cuza" University;Physical, Theoretical and Materials Chemistry adr:Nr. 11;;Bd. Carol 1, ;Iasi;;700506;Romania email;internet:dan.maftei^chem.uaic.ro title:Faculty of Chemistry tel;work:+40232-201307 tel;fax:+40232-201313 tel;cell:+40740-262227 x-mozilla-html:FALSE url:http://www.chem.uaic.ro/~danmaftei version:2.1 end:vcard --------------090805090503040201020206-- From owner-chemistry@ccl.net Wed Jul 11 04:49:00 2007 From: "Gijs Schaftenaar schaft : cmbi.ru.nl" To: CCL Subject: CCL: Visualizing vibrational data Message-Id: <-34719-070710150933-18495-zYvsLASn9misyiBgm1YzRw.@.server.ccl.net> X-Original-From: Gijs Schaftenaar Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 10 Jul 2007 20:39:55 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Gijs Schaftenaar [schaft{=}cmbi.ru.nl] Molden will display vibration output from Qchem ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden4.6.tar.gz Best Regards, Gijs Schaftenaar +----------------------------------------------------------------+ Gijs Schaftenaar, Dr. | Computational Drug Discovery, CMBI Email: | Radboud University of Nijmegen G.Schaftenaar[*]ncmls.ru.nl | Medical Centre / NCMLS, route 260 Tel. : +31 24 3619674 | Geert-Grooteplein 28 Fax : +31 24 3619395 | 6525 GA Nijmegen, The Netherlands +----------------------------------------------------------------+ On Mon, 9 Jul 2007, Raoul E Correa raoul##berkeley.edu wrote: > Date: Mon, 9 Jul 2007 13:49:40 -0400 > From: Raoul E Correa raoul##berkeley.edu > Reply-To: CCL Subscribers > To: "Schaftenaar, Gijs " > Subject: CCL: Visualizing vibrational data > > > Sent to CCL by: "Raoul E Correa" [raoul+*+berkeley.edu] > Hello, > > I was wondering if there is software which helps one visualize the motions of atoms along a vibrational mode, such as those described by a frequency calculation in any computational package. I run simulations on QChem but haven't found a program that will take the output and create animations of the actual vibrational mode. > > Does anyone know of such a stand-alone program? Or maybe a way to convert the output into something that another program (e.g. Molekel) could use? Thanks for the help! > > Raoul> > > From owner-chemistry@ccl.net Wed Jul 11 05:46:00 2007 From: "Ulrike Salzner salzner+*+fen.bilkent.edu.tr" To: CCL Subject: CCL:G: large NBO E2 energy values for antibonding-antibonding interactions Message-Id: <-34720-070711042758-28303-A43uUxcmGxbtseM5yHeKIg .. server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 11 Jul 2007 10:07:59 +0300 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner]_[fen.bilkent.edu.tr] Dear Reynier, The values you are getting are large because the energy difference in the denominator of second order perturbation theory formula is small. Since the overlap also substantial, you do not have a small perturbation. Therefore second order perturbation theory should not be applied. I think the results you are getting are telefon numbers. What is true is that the orbitals lie close in energy and they ovelap. This should be a physical fact you may use. Regards, Ulrike Salzner Reynier Suardiaz reynier.suardiaz- -gmail.com schrieb: > Sent to CCL by: "Reynier Suardiaz" [reynier.suardiaz#gmail.com] > > Dear CCL > I am obtaining large values of E2 for "antibonding-antibonding" interactions withing NBO methodology using NBO 3.0 in gaussian03. i.e. > > 120. BD*( 2) C 4 - C 5 /115. BD*( 2) C 2 - C 3 163.56 0.01 0.067 > 124. BD*( 2) C 6 - O 10 / 81. RY*( 6) C 6 1.49 0.80 0.114 > 124. BD*( 2) C 6 - O 10 / 99. RY*( 2) O 10 0.77 1.00 0.092 > 124. BD*( 2) C 6 - O 10 /115. BD*( 2) C 2 - C 3 164.68 0.01 0.079 > > E2 values of 163.56 and 164.68 kcal/mol... > > This is in O-O trans isomer of furfural, in O-O cis isomer there are not those large numbers. > Which can be the meaning of this numbers? Are those numbers correct? > > any suggestion would be appreciated > > Best regards > reynier> > > > > > From owner-chemistry@ccl.net Wed Jul 11 06:19:00 2007 From: "Caroline Norris cn29]_[sussex.ac.uk" To: CCL Subject: CCL: CASSCF symmetry Message-Id: <-34721-070711061628-10826-AACo/mpdprKz8QgjfYIiOA]|[server.ccl.net> X-Original-From: "Caroline Norris" Date: Wed, 11 Jul 2007 06:16:25 -0400 Sent to CCL by: "Caroline Norris" [cn29=-=sussex.ac.uk] Dear CCL, It appears that CASSCF does not provide the symmetry of excited states or the relative oscillator strengths of each excitation. What is the standard practice to ensure the correct state is obtained with respect to experimental data? Any information would be gratefully received. Yours, Caroline Norris From owner-chemistry@ccl.net Wed Jul 11 08:20:00 2007 From: "T. Daniel Crawford crawdad*_*exchange.vt.edu" To: CCL Subject: CCL:G: G03: Negative eigenvalue, but no imaginary frequencies Message-Id: <-34722-070710210317-20491-sZ0aopmznGkSL1n5yRqRYg#server.ccl.net> X-Original-From: "T. Daniel Crawford" Content-type: multipart/alternative; boundary="B_3266946190_3856148" Date: Tue, 10 Jul 2007 21:03:10 -0400 Mime-version: 1.0 Sent to CCL by: "T. Daniel Crawford" [crawdad^exchange.vt.edu] > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3266946190_3856148 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable The negative eigenvalues in your case almost certainly correspond to translations and/or rotations. After reporting these values, the Gaussian code then transforms the coordinates to a rotating-translating frame, thereby forcing the corresponding eigenvalues to zero. Thus, the remaining 3N-6 vibrational modes after projection could certainly all be real. Note also that the more tightly you converge the geometry optimization, the closer to zero the rotational and translational =B3frequencies=B2 will be. (Note also that, if you=B9re using a DFT approach like B3LYP, this also requires that you use a very dense integration grid.) -Daniel On 7/10/07 10:21 AM, "Stephen.Garrison . srnl.doe.gov" wrote: >=20 > Has anyone seen G03 perform a transition state optimization (with CalcAll= ) > with no constraints, find a stationary point with one non-zero, negative > eigenvalue (in this case -0.00447), and then find NO imaginary frequencie= s? > Does anyone have an idea of what went wrong or what is happening? >=20 > Here are some snippets from the end fo the file: >=20 > Berny optimization. > Use GDIIS/GDPIS optimizer. > Internal Forces: Max 0.000014071 RMS 0.000002532 > Search for a saddle point. > Step number 39 out of a maximum of 46 > All quantities printed in internal units (Hartrees-Bohrs-Radians) > Swaping is turned off. > Second derivative matrix not updated -- analytic derivatives used. > Eigenvalues --- -0.00447 0.00391 0.00510 0.01026 0.02635 > Eigenvalues --- 0.03313 0.03457 0.04197 0.04777 0.05408 > Eigenvalues --- 0.07590 0.09529 0.12116 0.13685 0.22436 > Eigenvalues --- 0.22531 0.23190 0.28322 0.37711 0.46845 > Eigenvalues --- 0.530671000.000001000.000001000.000001000.00000 > Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 > Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 > Eigenvalues --- 1000.00000 >=20 > Item Value Threshold Converged? > Maximum Force 0.000014 0.000015 YES > RMS Force 0.000003 0.000010 YES > Maximum Displacement 0.000020 0.000060 YES > RMS Displacement 0.000007 0.000040 YES >=20 > Low frequencies --- -12.5184 -6.3209 -0.0001 0.0005 0.0008 > 2.6758=20 > Low frequencies --- 70.3933 92.5242 122.4695 >=20 > Thanks for your help. >=20 --=20 T. Daniel Crawford Department of Chemistry crawdad]![vt.edu Virginia Tech www.chem.vt.edu/faculty/crawford.php Voice: 540-231-7760 FAX: 540-231-325= 5 -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt --B_3266946190_3856148 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Re: CCL:G: G03: Negative eigenvalue, but no imaginary frequencies</T= ITLE> </HEAD> <BODY> <FONT FACE=3D"Verdana, Helvetica, Arial"><SPAN STYLE=3D'font-size:12.0px'>The n= egative eigenvalues in your case almost certainly correspond to translations= and/or rotations.  After reporting these values, the Gaussian code the= n transforms the coordinates to a rotating-translating frame, thereby forcin= g the corresponding eigenvalues to zero.  Thus, the remaining 3N-6 vibr= ational modes after projection could certainly all be real.<BR> <BR> Note also that the more tightly you converge the geometry optimization, the= closer to zero the rotational and translational “frequencies” w= ill be.   (Note also that, if you’re using a DFT approach li= ke B3LYP, this also requires that you use a very dense integration grid.)<BR= > <BR> -Daniel<BR> <BR> On 7/10/07 10:21 AM, "Stephen.Garrison . srnl.doe.gov" <owner-= chemistry]![ccl.net> wrote:<BR> <BR> </SPAN></FONT><BLOCKQUOTE><FONT FACE=3D"Verdana, Helvetica, Arial"><SPAN STYL= E=3D'font-size:12.0px'><BR> Has anyone seen G03 perform a transition state optimization (with CalcAll) = with no constraints, find a stationary point with one non-zero, negative eig= envalue (in this case -0.00447), and then find NO imaginary frequencies? Doe= s anyone have an idea of what went wrong or what is happening? <BR> <BR> Here are some snippets from the end fo the file: <BR> <BR>  Berny optimization. <BR>  Use GDIIS/GDPIS optimizer. <BR>  Internal  Forces:  Max     0.000014071 = RMS     0.000002532 <BR>  Search for a saddle point. <BR>  Step number  39 out of a maximum of  46 <BR>  All quantities printed in internal units (Hartrees-Bohrs-Radians) <BR= >  Swaping is turned off. <BR>  Second derivative matrix not updated -- analytic derivatives used. <B= R>      Eigenvalues ---   -0.00447  &n= bsp;0.00391   0.00510   0.01026   0.02635 <BR>      Eigenvalues ---    0.03313 &nb= sp; 0.03457   0.04197   0.04777  0.05408 <BR>      Eigenvalues ---    0.07590 &nb= sp; 0.09529   0.12116   0.13685  0.22436 <BR>      Eigenvalues ---    0.22531 &nb= sp; 0.23190   0.28322   0.37711  0.46845 <BR>      Eigenvalues ---    0.530671000= .000001000.000001000.000001000.00000 <BR>      Eigenvalues --- 1000.000001000.000001000.0000= 01000.000001000.00000 <BR>      Eigenvalues --- 1000.000001000.000001000.0000= 01000.000001000.00000 <BR>      Eigenvalues --- 1000.00000 <BR> <BR>          Item   &nbs= p;           Value &n= bsp;   Threshold  Converged? <BR>  Maximum Force          &= nbsp;0.000014     0.000015     YES <= BR>  RMS     Force       = ;    0.000003     0.000010  &nb= sp; YES <BR>  Maximum Displacement    0.000020    &nb= sp;0.000060     YES <BR>  RMS     Displacement     0.00= 0007     0.000040     YES <BR> <BR>  Low frequencies ---  -12.5184   -6.3209   -0= .0001    0.0005    0.0008   2.6758 <= BR>  Low frequencies ---   70.3933   92.5242  122= .4695 <BR> <BR> Thanks for your help. <BR> <BR> </SPAN></FONT></BLOCKQUOTE><FONT FACE=3D"Verdana, Helvetica, Arial"><SPAN STY= LE=3D'font-size:12.0px'><BR> <BR> -- <BR> T. Daniel Crawford          &n= bsp;            =     Department of Chemistry<BR> crawdad]![vt.edu           =             &nbs= p;            Vi= rginia Tech<BR> www.chem.vt.edu/faculty/crawford.php  Voice: 540-231-7760  FAX: 5= 40-231-3255<BR>             &nb= sp;            &= nbsp;  --------------------<BR>  PGP Public Key at: <a href=3D"http://www.chem.vt.edu/chem-dept/crawford= /publickey.txt">http://www.chem.vt.edu/chem-dept/crawford/publickey.txt</a><= BR> </SPAN></FONT> </BODY> </HTML> --B_3266946190_3856148-- From owner-chemistry@ccl.net Wed Jul 11 09:13:00 2007 From: "fdu.xiaojf-*-gmail.com fdu.xiaojf-*-gmail.com" <owner-chemistry===server.ccl.net> To: CCL Subject: CCL: Where to find Lennard-Jones 6-12 potential parameters ? Message-Id: <-34723-070710114236-11099-ypVT4zBISehoQe4g3/MdLQ===server.ccl.net> X-Original-From: "fdu.xiaojf- -gmail.com" <fdu.xiaojf- -gmail.com> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Tue, 10 Jul 2007 22:44:49 +0800 MIME-Version: 1.0 Sent to CCL by: "fdu.xiaojf!=!gmail.com" [fdu.xiaojf!=!gmail.com] Hi all, Where to find Lennard-Jones 6-12 potential parameters of gases and solids ? I have searched the web, and there are many explanations of L-J potential, but no collection of L-J 6-12 potential parameters for specific species. Thanks. From owner-chemistry@ccl.net Wed Jul 11 09:30:00 2007 From: "DSprous[]redpointbio.com" <owner-chemistry{=}server.ccl.net> To: CCL Subject: CCL: Converting structures to IUPAC names Message-Id: <-34724-070710125533-14019-KPPi6HPLg9IjMnTD0WXSQQ{=}server.ccl.net> X-Original-From: <DSprous(!)redpointbio.com> Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 10 Jul 2007 12:22:40 -0400 MIME-Version: 1.0 Sent to CCL by: [DSprous.-x-.redpointbio.com] Dear All: The three options for name to structure and structure to name conversion that I am aware of are offered by: Cambridgesoft ACD OpenEyes Dennis G. Sprous, PhD Chemoinformatics/Computational Chemistry RedPointBio Inc. 7 Graphics Drive Ewing NJ 08628 609-637-9700 -----Original Message----- > From: owner-chemistry-x-ccl.net [mailto:owner-chemistry-x-ccl.net] Sent: Thursday, July 05, 2007 11:51 AM To: Dennis Sprous Subject: CCL: Converting structures to IUPAC names Sent to CCL by: Arnab Chakrabarty [r.arnab,+,gmail.com] Hi, I guess ChemOffice (http://www.cambridgesoft.com/software/ChemOffice/) has that functionality. Thanks Arnab andras.borosy/./givaudan.com wrote: > > Dear Colleagues, > > Does anyone know an application which is capable to convert structures > to IUPAC names of a larger database? > > Best regards, > > Dr. András Péter Borosy > Scientific Modelling Expert > Fragrance Research > Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf > - Switzerland > T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.comhttp://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 Wed Jul 11 10:07:00 2007 From: "xiaojf_-_mail.shcnc.ac.cn xiaojf_-_mail.shcnc.ac.cn" <owner-chemistry::server.ccl.net> To: CCL Subject: CCL: Where to find Lennard-Jones 6-12 potential parameters ? Message-Id: <-34725-070711075546-21512-Gi3azJQW7OgxmNjVxt1d9Q::server.ccl.net> X-Original-From: "xiaojf=-=mail.shcnc.ac.cn" <xiaojf=-=mail.shcnc.ac.cn> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 11 Jul 2007 19:02:36 +0800 MIME-Version: 1.0 Sent to CCL by: "xiaojf^mail.shcnc.ac.cn" [xiaojf^mail.shcnc.ac.cn] Hi all, Where to find Lennard-Jones 6-12 potential parameters of gases and solids ? I have searched the web, and there are many explanations of L-J potential, but no collection of L-J 6-12 potential parameters for specific species. Thanks. From owner-chemistry@ccl.net Wed Jul 11 10:40:00 2007 From: "Stephen.Garrison(-)srnl.doe.gov" <owner-chemistry+*+server.ccl.net> To: CCL Subject: CCL:G: G03: Negative eigenvalue, but no imaginary frequencies Message-Id: <-34726-070711102659-25775-6B+q8iuLoo9qqyczmVCjlw+*+server.ccl.net> X-Original-From: Stephen.Garrison[A]srnl.doe.gov Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 11 Jul 2007 10:26:26 -0400 MIME-Version: 1.0 Sent to CCL by: Stephen.Garrison^^^srnl.doe.gov A couple of notes: 1. I had been doing a normal optimization and thought it might be a convergence issue. But, as noted by the thresholds below, I switched to the "tight" optimization criteria for this calculation and the issue remains. 2. I am using the ultrafine grid for the B3LYP/DFT calculation. 3. There are 9 atoms in the system for a total of 21 vibrational modes. There are 21 eigenvalues below and 21 reported frequencies. I would assume that Gaussian is already kicking out the 3 translational and 3 rotational modes during the optimization (but maybe I am wrong or maybe it is kicking out the wrong eigenvalues). Any time I have seen an issue with mistaken translational or rotational modes before, the magnitude of the eigenvalue has been significantly closer to zero, on the order of 0.00001. The value below is 2 orders of magnitude larger. Any other thoughts or comments? "T. Daniel Crawford crawdad*_*exchange.vt.edu" <owner-chemistry[#]ccl.net> Sent by: owner-chemistry[#]ccl.net 07/10/2007 09:03 PM Please respond to "CCL Subscribers" <chemistry[#]ccl.net> To "Garrison, Stephen L. " <stephen.garrison[#]srnl.doe.gov> cc Subject CCL:G: G03: Negative eigenvalue, but no imaginary frequencies The negative eigenvalues in your case almost certainly correspond to translations and/or rotations. After reporting these values, the Gaussian code then transforms the coordinates to a rotating-translating frame, thereby forcing the corresponding eigenvalues to zero. Thus, the remaining 3N-6 vibrational modes after projection could certainly all be real. Note also that the more tightly you converge the geometry optimization, the closer to zero the rotational and translational “frequencies†will be. (Note also that, if you’re using a DFT approach like B3LYP, this also requires that you use a very dense integration grid.) -Daniel On 7/10/07 10:21 AM, "Stephen.Garrison . srnl.doe.gov" <owner-chemistry:+:ccl.net> wrote: Has anyone seen G03 perform a transition state optimization (with CalcAll) with no constraints, find a stationary point with one non-zero, negative eigenvalue (in this case -0.00447), and then find NO imaginary frequencies? Does anyone have an idea of what went wrong or what is happening? Here are some snippets from the end fo the file: Berny optimization. Use GDIIS/GDPIS optimizer. Internal Forces: Max 0.000014071 RMS 0.000002532 Search for a saddle point. Step number 39 out of a maximum of 46 All quantities printed in internal units (Hartrees-Bohrs-Radians) Swaping is turned off. Second derivative matrix not updated -- analytic derivatives used. Eigenvalues --- -0.00447 0.00391 0.00510 0.01026 0.02635 Eigenvalues --- 0.03313 0.03457 0.04197 0.04777 0.05408 Eigenvalues --- 0.07590 0.09529 0.12116 0.13685 0.22436 Eigenvalues --- 0.22531 0.23190 0.28322 0.37711 0.46845 Eigenvalues --- 0.530671000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.00000 Item Value Threshold Converged? Maximum Force 0.000014 0.000015 YES RMS Force 0.000003 0.000010 YES Maximum Displacement 0.000020 0.000060 YES RMS Displacement 0.000007 0.000040 YES Low frequencies --- -12.5184 -6.3209 -0.0001 0.0005 0.0008 2.6758 Low frequencies --- 70.3933 92.5242 122.4695 Thanks for your help. -- T. Daniel Crawford Department of Chemistry crawdad:+:vt.edu Virginia Tech www.chem.vt.edu/faculty/crawford.php Voice: 540-231-7760 FAX: 540-231-3255 -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt From owner-chemistry@ccl.net Wed Jul 11 11:20:01 2007 From: "Yuan Zhao ccl*mail.sioc.ac.cn" <owner-chemistry.@.server.ccl.net> To: CCL Subject: CCL: Where to find FDA drug database Message-Id: <-34727-070711103945-1207-4rueGL44kDMmBcaj4lb2XA.@.server.ccl.net> X-Original-From: "Yuan Zhao" <ccl###mail.sioc.ac.cn> Date: Wed, 11 Jul 2007 10:39:42 -0400 Sent to CCL by: "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] Hi all, I wonder how many drugs FDA have approved till now or this year. If possible, where can I download the FDA drug database in sd, mol or other chemical formats? Does anyone know how many drugs in FDA are fit for Lipinski rule of five? Any clue will be appreciate. Thanks. Steven From owner-chemistry@ccl.net Wed Jul 11 12:57:00 2007 From: "Abdul Hameed, MohamedDiwanMo mabdu3,,email.uky.edu" <owner-chemistry{=}server.ccl.net> To: CCL Subject: CCL: Where to find FDA drug database Message-Id: <-34728-070711125215-20008-5yEiJFSpWRD6xA5X8eka8w{=}server.ccl.net> X-Original-From: "Abdul Hameed, MohamedDiwanMo" <mabdu3++email.uky.edu> Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_62D3F106CB16C34D825A1B75EFBA6839D5929160EX7FM04adukyedu_" Date: Wed, 11 Jul 2007 12:20:37 -0400 MIME-Version: 1.0 Sent to CCL by: "Abdul Hameed, MohamedDiwanMo" [mabdu3[#]email.uky.edu] --_000_62D3F106CB16C34D825A1B75EFBA6839D5929160EX7FM04adukyedu_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hello, The Drug Bank website has a nicely annotated collection of nearly 1010 FDA = approved drugs. The website shows we can download them as sdf file. Below i= s the link : http://redpoll.pharmacy.ualberta.ca/drugbank/cgi-bin/download.cgi HTH, Cheers, Mohamed Diwan Graduate student, University of Kentucky. -----Original Message----- > From: owner-chemistry _ ccl.net [mailto:owner-chemistry _ ccl.net] Sent: Wednesday, July 11, 2007 10:40 AM To: Abdul Hameed, MohamedDiwanMo Subject: CCL: Where to find FDA drug database Sent to CCL by: "Yuan Zhao" [ccl=3D-=3Dmail.sioc.ac.cn] Hi all, I wonder how many drugs FDA have approved till now or this year. If possible, where can I download the FDA drug database in sd, mol or other chemical formats? Does anyone know how many drugs in FDA are fit for Lipinski rule of five? Any clue will be appreciate. Thanks. Steven -=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--_000_62D3F106CB16C34D825A1B75EFBA6839D5929160EX7FM04adukyedu_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable <html xmlns:o=3D"urn:schemas-microsoft-com:office:office" xmlns:w=3D"urn:sc= hemas-microsoft-com:office:word" xmlns=3D"http://www.w3.org/TR/REC-html40"> <head> <META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; charset=3Dus-ascii"= > <meta name=3DGenerator content=3D"Microsoft Word 11 (filtered medium)"> <style> <!-- /* Font Definitions */ _ font-face {font-family:SimSun; panose-1:2 1 6 0 3 1 1 1 1 1;} _ font-face {font-family:"\ _ SimSun"; panose-1:2 1 6 0 3 1 1 1 1 1;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; margin-bottom:.0001pt; text-align:justify; text-justify:inter-ideograph; font-size:10.5pt; font-family:"Times New Roman";} a:link, span.MsoHyperlink {color:blue; text-decoration:underline;} a:visited, span.MsoHyperlinkFollowed {color:purple; text-decoration:underline;} p.MsoPlainText, li.MsoPlainText, div.MsoPlainText {margin:0in; margin-bottom:.0001pt; font-size:9.0pt; font-family:SimSun;} /* Page Definitions */ _ page Section1 {size:595.3pt 841.9pt; margin:1.0in 126.65pt 1.0in 126.65pt; layout-grid:15.6pt;} div.Section1 {page:Section1;} --> </style> </head> <body lang=3DZH-CN link=3Dblue vlink=3Dpurple style=3D'text-justify-trim:pu= nctuation'> <div class=3DSection1 style=3D'layout-grid:15.6pt'> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Hello,<o:p></o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>The Drug Bank website has a ni= cely annotated collection of nearly 1010 FDA approved drugs. The website shows w= e can download them as sdf file. Below is the link :<o:p></o:p></span></font>= </p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><a href=3D"http://redpoll.pharmacy.ualberta.ca/drugbank/cgi-bin/download.cgi">= http://redpoll.pharmacy.ualberta.ca/drugbank/cgi-bin/download.cgi</a><o:p><= /o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>HTH,<o:p></o:p></span></font><= /p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Cheers,<o:p></o:p></span></fon= t></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Mohamed Diwan<o:p></o:p></span= ></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Graduate student,<o:p></o:p></= span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>University of Kentucky.<o:p></= o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>-----Original Message-----<br> > From: owner-chemistry _ ccl.net [mailto:owner-chemistry _ ccl.net] <br> Sent: Wednesday, July 11, 2007 10:40 AM<br> To: Abdul Hameed, MohamedDiwanMo<br> Subject: CCL: Where to find FDA drug database</span></font><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial= '><o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Sent to CCL by: "Yuan&nbs= p; Zhao" [ccl=3D-=3Dmail.sioc.ac.cn]<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Hi all,<o:p></o:p></span></fon= t></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>  I wonder how many drugs= FDA have approved till now or this year.<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>If possible, where can I downl= oad the FDA drug database in sd, mol<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>or other chemical formats? Doe= s anyone know how many drugs in FDA<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>are fit for Lipinski rule of f= ive? Any clue will be appreciate.<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Thanks.<o:p></o:p></span></fon= t></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Steven<o:p></o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>-=3D This is automatically add= ed to each message by the mailing script =3D-<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>To recover the email address o= f the author of the message, please change<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>the strange characters on the = top line to the _ sign. You can also<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>look up the X-Original-From: l= ine in the mail header.<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>     =<o:p></o:p></span></font></= p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>     <o:p></o:p></span></font></p= > <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Subscribe/Unsubscribe:<o:p></o= :p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>     <o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Before posting, check wait tim= e at: http://www.ccl.net<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Job: http://www.ccl.net/jobs<o= :p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'<o:p></o:p></span= ></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)<o:p></o:p></s= pan></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>If your mail bounces from CCL = with 5.7.1 error, check:<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>     <o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'<o:p></o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+= -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+<o:p></o:p></span></font></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> <p class=3DMsoPlainText><font size=3D2 face=3DArial><span lang=3DEN-US style=3D'font-size:11.0pt;font-family:Arial'><o:p> </o:p></span></font= ></p> </div> </body> </html> --_000_62D3F106CB16C34D825A1B75EFBA6839D5929160EX7FM04adukyedu_-- From owner-chemistry@ccl.net Wed Jul 11 13:38:00 2007 From: "Brian Williams williams__bucknell.edu" <owner-chemistry]-[server.ccl.net> To: CCL Subject: CCL: Where to find Lennard-Jones 6-12 potential parameters ? Message-Id: <-34729-070711120547-7711-2BZu1+asIyv/G9iU9IfMUQ]-[server.ccl.net> X-Original-From: Brian Williams <williams[A]bucknell.edu> Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Wed, 11 Jul 2007 11:29:17 -0400 Mime-Version: 1.0 Sent to CCL by: Brian Williams [williams * bucknell.edu] A very old source for some species is Table 1A in the Appendix of " Molecular Theory of Gases and Liquids" by Hirschfelder, Curtiss and Bird. There are likely more recent ones. Brian Williams, Chemistry, Bucknell University t 10:44 AM 7/10/2007, you wrote: >Sent to CCL by: "fdu.xiaojf!=!gmail.com" [fdu.xiaojf!=!gmail.com] > >Hi all, > >Where to find Lennard-Jones 6-12 potential parameters of gases and >solids ? I have searched the web, and there are many explanations of L-J >potential, but no collection of L-J 6-12 potential parameters for specific >species. > >Thanks.http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Wed Jul 11 14:33:02 2007 From: "DSprous-.-redpointbio.com" <owner-chemistry],[server.ccl.net> To: CCL Subject: CCL: Where to find FDA drug database Message-Id: <-34730-070711134114-14063-kg9m3NOCg3GVyFgnNKeTdw],[server.ccl.net> X-Original-From: <DSprous|redpointbio.com> Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 11 Jul 2007 13:08:24 -0400 MIME-Version: 1.0 Sent to CCL by: [DSprous*redpointbio.com] In reply to "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] query summarized as: "I wonder how many drugs FDA have approved till now or this year?" To my knowledge: The FDA Orange Book (http://www.fda.gov/cder/ob/) is closest publicly available answer to this question. It is a list of approved drug formulations and does not have structures. Further, since it is a list of approved formulations, children's motrin is distinct from adult strength which is different from extra strength. The FDA apparently simply does not seem to be interested in an actual molecular database of approved active ingredients. You would need to download a copy of the list, develop a script to generate a unique list of active ingredients and then use something like LexiChem to convert the chemical and trade names to SMILES. This gives one about 1300 to 1400 compounds. An alternative which is easier to work with is the DrugBank (http://redpoll.pharmacy.ualberta.ca/drugbank/) datasets maintained by Wishart [University of Alberta]. This too is a list of ~1300 to 1400 compounds. If anyone knows better public sources, please post. Dennis G. Sprous, PhD Chemoinformatics/Computational Chemistry RedPointBio Inc. 7 Graphics Drive Ewing NJ 08628 609-637-9700 -----Original Message----- > From: owner-chemistry|,|ccl.net [mailto:owner-chemistry|,|ccl.net] Sent: Wednesday, July 11, 2007 10:40 AM To: Dennis Sprous Subject: CCL: Where to find FDA drug database Sent to CCL by: "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] Hi all, I wonder how many drugs FDA have approved till now or this year. If possible, where can I download the FDA drug database in sd, mol or other chemical formats? Does anyone know how many drugs in FDA are fit for Lipinski rule of five? Any clue will be appreciate. Thanks. Stevenhttp://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 Wed Jul 11 23:00:00 2007 From: "Raji Raji raji[-]anal.chem.tohoku.ac.jp" <owner-chemistry%%server.ccl.net> To: CCL Subject: CCL:G: G03-TDDFT error termination Message-Id: <-34731-070711225851-24886-H7xadAG+wymJnFVC2jaVfA%%server.ccl.net> X-Original-From: "Raji Raji" <raji()anal.chem.tohoku.ac.jp> Date: Wed, 11 Jul 2007 22:58:48 -0400 Sent to CCL by: "Raji Raji" [raji|a|anal.chem.tohoku.ac.jp] Dear CCL Members, My TDDFT calculation on a hydrogen bonded system terminated with an error. Please do find the part input and out put files below. It seems the error in the Link commands. I checked in the gaussian manual, it says that the L914.exe corresponds to CI-Singles, RPA and Zindo excited states; SCF stability. But dont know how to solve this problem. Any help will be thankfully acknowledged. %Chk=ex.chk %NProc=xx %Mem=xx TD(NStates=25, Singlets, Direct) B3LYP/6-31+G(d,p) test SCRF=(CPCM, Solvent=Water) Excited Singlet state calculation (CPCM-Water) 0 1 1 5.674463 -1.230794 36.004465 ..... 100 initial guesses have been made. Convergence on wavefunction: 0.001000000000000 Iteration 1 Dimension 100 NMult 100 CISAX will form 100 AO SS matrices at one time. Unable to match L and R vectors in BiOrth. Error termination via Lnk1e in /usr/ap/g03/l914.exe at Wed Jul 11 16:57:36 2007. Job cpu time: 0 days 3 hours 46 minutes 25.8 seconds. File lengths (MBytes): RWF= 965 Int= 0 D2E= 0 Chk= 5 Scr= 1