From owner-chemistry@ccl.net Thu Feb 14 04:26:00 2008 From: "Giulia Caron giulia.caron##unito.it" To: CCL Subject: CCL: from SMILES/MDL to gif/png Message-Id: <-36288-080214040217-7123-YbbQtOuAaOtIs8uD7evOQw{:}server.ccl.net> X-Original-From: "Giulia Caron" Date: Thu, 14 Feb 2008 04:02:12 -0500 Sent to CCL by: "Giulia Caron" [giulia.caron . unito.it] Dear all, I am looking for a free generator (for Web-based applications) of 2D chemical structures in gif/png/... format from a SMILES/MDL input. Best regards Giulia From owner-chemistry@ccl.net Thu Feb 14 07:50:01 2008 From: "andrea spitaleri spitaleri.andrea(_)hsr.it" To: CCL Subject: CCL: MonteCarlo: free software Message-Id: <-36289-080214074308-12807-emnUJGym9/gfN1qaqCvh4w[#]server.ccl.net> X-Original-From: andrea spitaleri Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 14 Feb 2008 12:01:19 +0100 MIME-Version: 1.0 Sent to CCL by: andrea spitaleri [spitaleri.andrea,+,hsr.it] Dear all, while there are plenty of free MD software around (gromacs, amber, namd), I am wondering whether there are free conformational searching software using Montecarlo/Metropolis algorithm. Any suggestions? For instance, how good is Tinker? thanks in advance Regards andrea -- ------------------------------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 ------------------------------- From owner-chemistry@ccl.net Thu Feb 14 08:34:00 2008 From: "zborowsk^chemia.uj.edu.pl" To: CCL Subject: CCL: Scaling of Raman Frequencies Message-Id: <-36290-080214082957-30363-ar9tBHsI5oWy8YJEwBLwzw{}server.ccl.net> X-Original-From: zborowsk_+_chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Thu, 14 Feb 2008 14:29:26 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: zborowsk[#]chemia.uj.edu.pl > I have a few questions concerning the calculation of raman frequencies. > The > first is, should one consider the IR scaling factors to be valid for > Raman? > Raman is essentially an emission phenomenon while IR frequencies are an > abosorbance phenomenon. > I do not understand where is the problem (if we consider the frequencies scaling, not intensities)? It is true that Raman and IR are based on two (very) different phenomena. But the frequencies of normal modes are the same and they do not depend on emission or absorption. There is no thing like "scaling factor for IR frequencies". You scale frequencies of normal modes, not IR frequencies or Raman frequencies > My second question is, if Raman frequencies should be scaled, should Raman > frequencies determined by incorporation of solvent effects also be scaled? > > Any thoughts on this are welcome. > > > Mark > -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk]*[chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70 From owner-chemistry@ccl.net Thu Feb 14 10:40:00 2008 From: "Ivanciuc, Ovidiu I. oiivanci###utmb.edu" To: CCL Subject: CCL: from SMILES/MDL to gif/png Message-Id: <-36291-080214103822-5272-zAlRR4w4twQCrbh6X+RJVA*server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 14 Feb 2008 09:36:38 -0600 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci-$-utmb.edu] >>I am looking for a free generator (for Web-based applications) >> of 2D chemical structures in gif/png/... format from a SMILES/MDL = input.=20 Try the NCI GIF/PNG-Creator for 2D Plots of Chemical Structures http://cactus.nci.nih.gov/services/gifcreator/ Ovidiu From owner-chemistry@ccl.net Thu Feb 14 11:14:00 2008 From: "Cory Pye cpye!^!crux.smu.ca" To: CCL Subject: CCL: Scaling of Raman Frequencies Message-Id: <-36292-080213193612-3153-Hn8UzV3N3uiBa2JvLbsOYA,server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 13 Feb 2008 19:31:40 -0400 (AST) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye**crux.smu.ca] On Wed, 13 Feb 2008, Mark Zottola mzottola]^[gmail.com wrote: > I have a few questions concerning the calculation of raman frequencies. The > first is, should one consider the IR scaling factors to be valid for Raman? > Raman is essentially an emission phenomenon while IR frequencies are an > abosorbance phenomenon. Yes. The Raman frequencies should be the same as the IR frequencies, within the harmonic approximation. Any instances of non-coincidence point to some other effect going on. Therefore, the same scaling factors should also apply. The statement that Raman is essentially an emission phenomenon is true; however, the frequency that is actually reported is the difference between the frequency of light used (typically, a laser line, or in the older literature, a mercury arc source with filters) versus that which is Raman scattered. It is not the same thing as a absorption versus an emission spectra (much more complicated), because the "virtual state" only sticks around for a ps or so, and thus the system doesn't have time to do anything fancy (IC,ISC,...). > > My second question is, if Raman frequencies should be scaled, should Raman > frequencies determined by incorporation of solvent effects also be scaled? > It depends on the reason for scaling. Typically scale factors are derived for gas-phase molecules (experiment and theory) and correct for both deficiencies in level and deficiencies in the harmonic approximation. For something like an OH or CH stretching, there is a very large anharmonic contribution. Hartree-Fock scaling factors are also accounting for the neglect of electron correlation, which is very important for motions which involve homolytic cleavage (i.e. C-H). For M-O stretching modes in M(H2O)n m+ (aq), I have found that the frequencies are underestimated, not overestimated. For these modes, the stretching involves a heterolytic cleavage (electron pair remains intact, at least near the equilibrium distance) so correlation is not a factor, and anharmonicity is rather small (as determined by the T-dependence of frequencies in solution). In this case, one can scale for the effect of the medium, or include a second hydration sphere. We didn't find that scaling was that useful for the modes that we were interested in. For more details, you can check out some of my papers (esp. JPC 1998) http://www.ap.smu.ca/~cpye/CV/index.html > Mark > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye~!~crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Thu Feb 14 11:59:00 2008 From: "Giulio Vistoli giulio.vistoli(~)unimi.it" To: CCL Subject: CCL: MonteCarlo: free software Message-Id: <-36293-080214095758-1789-SJ35gl5Imeg2A5y1+np5eA*o*server.ccl.net> X-Original-From: Giulio Vistoli Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=iso-8859-1; reply-type=original Date: Thu, 14 Feb 2008 15:09:23 +0100 MIME-version: 1.0 Sent to CCL by: Giulio Vistoli [giulio.vistoli-,-unimi.it] Dear Andrea, VEGA software (freely downloadable at http://www.ddl.unimi.it/) can perform conformational analyses using Montecarlo/Metropolis algorithm. Moreover, VEGA automatically recognizes the rotatable bonds, implements many force fields, and performs also systematic searches or totally random searches. Best regards Giulio Vistoli ----- Original Message ----- > From: "andrea spitaleri spitaleri.andrea(_)hsr.it" To: "Vistoli, Giulio " Sent: Thursday, February 14, 2008 12:01 PM Subject: CCL: MonteCarlo: free software > > Sent to CCL by: andrea spitaleri [spitaleri.andrea,+,hsr.it] > Dear all, > while there are plenty of free MD software around (gromacs, amber, namd), > I am wondering whether > there are free conformational searching software using > Montecarlo/Metropolis algorithm. > Any suggestions? For instance, how good is Tinker? > > thanks in advance > > Regards > > andrea > > > > -- > ------------------------------- > Andrea Spitaleri PhD > Dulbecco Telethon Institute > c/o DIBIT Scientific Institute > Biomolecular NMR, 1B4 > Via Olgettina 58 > 20132 Milano (Italy) > http://biomolecularnmr.ihsr.dom/ > Tel: 0039-0226434348/5622/3497/4922 > Fax: 0039-0226434153 > -------------------------------> > > From owner-chemistry@ccl.net Thu Feb 14 12:34:01 2008 From: "Hemant Kumar Srivastava hemantkrsri:gmail.com" To: CCL Subject: CCL: Transition Dipole Moment Calculation Message-Id: <-36294-080214120124-24045-teIfobzhWhpwliijlQKACA]~[server.ccl.net> X-Original-From: "Hemant Kumar Srivastava" Date: Thu, 14 Feb 2008 12:01:20 -0500 Sent to CCL by: "Hemant Kumar Srivastava" [hemantkrsri^gmail.com] Dear Researchers, I want to know how to calculate the Transition Dipole Moment? This is a new topic for me, so if anybody know some papers or tutorials on it please help me. Thanks a lot in advance With kind regards, Hemant ================================ From owner-chemistry@ccl.net Thu Feb 14 13:11:00 2008 From: "Lukasz Cwiklik cwiklik . gmail.com" To: CCL Subject: CCL: MonteCarlo: free software Message-Id: <-36295-080214130938-5859-QAZDzgJOrTcyk2A+9lVLIQ .. server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 14 Feb 2008 20:09:24 +0200 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik.:.gmail.com] On Thu, Feb 14, 2008 at 1:01 PM, andrea spitaleri spitaleri.andrea(_)hsr.it wrote: > Sent to CCL by: andrea spitaleri [spitaleri.andrea,+,hsr.it] > Dear all, > while there are plenty of free MD software around (gromacs, amber, namd), I am wondering whether > there are free conformational searching software using Montecarlo/Metropolis algorithm. > Any suggestions? For instance, how good is Tinker? Dear Andrea, Take a look at Towhee (http://towhee.sourceforge.net). It is a huge package with many force-fields being available. From the web page: "Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling." Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Thu Feb 14 15:12:00 2008 From: "aa aa*_*chemaxon.hu" To: CCL Subject: CCL: from SMILES/MDL to gif/png Message-Id: <-36296-080214150536-15282-DKwUDmLUpsr5uDvFVFM7BQ+/-server.ccl.net> X-Original-From: aa Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 14 Feb 2008 15:05:22 -0500 MIME-Version: 1.0 Sent to CCL by: aa [aa_._chemaxon.hu] HI Giula, You can use Marvin for this, I am told it does quite well here, you can try image export from this online implementation (http://www.chemaxon.com/demosite/marvin/index.html). Through the API (http://www.chemaxon.com/marvin/help/developer/beans/api/index.html) you have much control of structure and image properties and Standardizer (http://www.chemaxon.com/product/standardizer.html) can be used to apply chemical business rules to the set prior to generation. These would be free for free webpages and free for Academic Package (personal license) or Academic Web if for campus wide access, more information and signup here: http://www.chemaxon.com/prices.html Cheers Alex Alex Allardyce, Mktg Dir, ChemAxon Giulia Caron giulia.caron##unito.it wrote: > Sent to CCL by: "Giulia Caron" [giulia.caron . unito.it] > Dear all, > > I am looking for a free generator (for Web-based applications) of 2D chemical structures in gif/png/... format from a SMILES/MDL input. > > Best regards > > Giulia> > > From owner-chemistry@ccl.net Thu Feb 14 15:47:01 2008 From: "Greg Warren greg!=!eyesopen.com" To: CCL Subject: CCL: from SMILES/MDL to gif/png Message-Id: <-36297-080214125802-28945-gPdxW3MWJDw6WRh6ww7CWw#,#server.ccl.net> X-Original-From: Greg Warren Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 14 Feb 2008 10:57:53 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg/a\eyesopen.com] Dear Giulia, OpenEye Scientific Software, Inc. has a toolkit (Ogham) to do this. When used in combination with Ogham, another toolkit (Lexichem) can be used to convert chemical names into 2D chemical structures. Our software is free of charge to academic and non-profit researchers. The academic license link is provided below. http://www.eyesopen.com/forms/academic_license_app.php Regards, Greg -- ======================================== Gregory Warren, PhD OpenEye Scientific Software, Inc 9 Bisbee Court, Suite D Santa Fe, NM 87508 (505) 473-7385 ext 50 mailto:greg#%#eyesopen.com ======================================== Giulia Caron giulia.caron##unito.it wrote: > Sent to CCL by: "Giulia Caron" [giulia.caron . unito.it] > Dear all, > > I am looking for a free generator (for Web-based applications) of 2D chemical structures in gif/png/... format from a SMILES/MDL input. > > Best regards > > Giulia> > > From owner-chemistry@ccl.net Thu Feb 14 18:08:01 2008 From: "Wolf-D.Ihlenfeldt wdi- -xemistry.com" To: CCL Subject: CCL: from SMILES/MDL to gif/png Message-Id: <-36298-080214180637-10457-RtUHdgPHJRAIkBfWgbV7TA**server.ccl.net> X-Original-From: "Wolf-D.Ihlenfeldt" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 15 Feb 2008 00:06:18 +0100 MIME-Version: 1.0 Sent to CCL by: "Wolf-D.Ihlenfeldt" [wdi .. xemistry.com] Giulia, yes, there is such an application - our Web depiction toolkit does = exactly what you need. The 2D layout algorithm is the same on as used, for = example, in PubChem and is probably the best in the industry. Another poster mentioned the Gifcreator service at NCI - the underlying software is = again the same, though in a slightly outdated version. A demo set-up, which also allows you to test with your own SMILES = strings or other input data, can be accessed at www.xemistry.com/molmagic. The software is free for academia (qualifying academic users will still = need to sign a licensing agreement detailing acceptable use), and may be used = to implement internal or public Web services which do not generate revenue. Commercial licenses are of course also available.=20 W. D. Ihlenfeldt Xemistry GmbH wdi . xemistry.com --- xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. = Ihlenfeldt Address: Auf den Stieden 8, D-35094 Lahntal, Germany Ust.-Id. No. DE 184/93908 : HR Marburg B4713 : EU Ust-Id. No. DE21531632 = : DUNS 34-400-1719=20 > -----Original Message----- > From: owner-chemistry . ccl.net [mailto:owner-chemistry . ccl.net]=20 > Sent: Thursday, February 14, 2008 10:02 AM > To: Ihlenfeldt, Wolf D > Subject: CCL: from SMILES/MDL to gif/png >=20 >=20 > Sent to CCL by: "Giulia Caron" [giulia.caron . unito.it] Dear all, >=20 > I am looking for a free generator (for Web-based=20 > applications) of 2D chemical structures in gif/png/... format=20 > from a SMILES/MDL input.=20 >=20 > Best regards >=20 > Giulia >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing=20 > script =3D- To recover the email address of the author of the=20 > message, please change the strange characters on the top line=20 > to the . sign. You can also look up the X-Original-From: line=20 > in the mail header. >=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20> Conferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/ >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl,=20 > Password: search) >=20>=20>=20 >=20 >=20 From owner-chemistry@ccl.net Thu Feb 14 19:29:01 2008 From: "DIEGOI GOMEZ darkego21^_^yahoo.com" To: CCL Subject: CCL:G: rotation of an adsorbate Message-Id: <-36299-080214191051-4358-n7gdjvDA/CAzq5h8q9m3KQ^^^server.ccl.net> X-Original-From: DIEGOI GOMEZ Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-262750834-1203034205=:82670" Date: Thu, 14 Feb 2008 16:10:05 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: DIEGOI GOMEZ [darkego21#yahoo.com] --0-262750834-1203034205=:82670 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit hello!! if you are using Gaussian, you can try to freeze each cartesian coordinate of each atom that you want and then let the others free. so you can do an relaxed or normal scan on any coordenate, for example the dihedral for rotations. (excuse me for my english if any mistake was written, I'm just learning it) "soumya samineni soumya_samineni=rediffmail.com" wrote: Sent to CCL by: "soumya samineni" [soumya_samineni=rediffmail.com] Hi all, I am trying to generate the PES of the adsorption of methane over Pt surface for a bench mark calcualtion. Translation of methane was no problem. But I am not able to genarate input where in i can rotate the methane only and leave the surface fixed .. I hope some one will help me how to go about it thanx in advance soumyahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtDiego Armando Gómez Hernández Licenciado en Química Universidad Distrital Francisco José de Caldas Bogotá-Colombia --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-262750834-1203034205=:82670 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit hello!!

if you are using Gaussian, you can try  to freeze each cartesian coordinate of each atom that you want and  then let the others free. so you can do an relaxed or normal scan  on any coordenate,  for  example the dihedral for rotations.
(excuse me for my english  if any mistake was written, I'm just learning it)

"soumya samineni soumya_samineni=rediffmail.com" <owner-chemistry * ccl.net> wrote:

Sent to CCL by: "soumya samineni" [soumya_samineni=rediffmail.com]
Hi all,
I am trying to generate the PES of the adsorption of methane over Pt surface for a bench mark calcualtion.
Translation of methane was no problem. But I am not able to genarate input where in i can rotate the methane only and leave the surface fixed ..
I hope some one will help me how to go about it

thanx in advance
soumya







Diego Armando Gómez Hernández
Licenciado en Química
Universidad Distrital Francisco José de Caldas
Bogotá-Colombia

Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-262750834-1203034205=:82670-- From owner-chemistry@ccl.net Thu Feb 14 22:00:00 2008 From: "Jerome Baudry jerome,scs.uiuc.edu" To: CCL Subject: CCL: vHTS: DOCK or AUTODOCK ? Message-Id: <-36300-080214215827-10863-OJSpghFBbmnSkXBjUNEsyQ(-)server.ccl.net> X-Original-From: "Jerome Baudry" Date: Thu, 14 Feb 2008 21:58:24 -0500 Sent to CCL by: "Jerome Baudry" [jerome=scs.uiuc.edu] Dear All I have been using commercial applications to perform virtual high throughput screening of virtual databases of compounds (a la ZINC) in protein models. I have access to a bunch of processors for embarrassingly parallel calculations, but the databases I want to screen are large. I would like to use free academic code, but it is not clear if DOCK (UCSF) or AUTODOCK (Scripps) will be able to process large databases of compounds - 700K cmpds or larger - in a reasonable time. I have seen results with AUTODOCK used to screen databases, but the published speed was about 1000 molecules per week on 32 procs, which is way slower that with, say, LigandFit (30K cmpds / day on 16 procs in my experience). I have not seen benchmark for DOCK in vHTS mode. Now I understand that speed is not everything, and that quality of the binding pose is important, but I am looking at screening very large databases and I first want to do it in a reasonable time. I can eventually spend more time redocking the top of the large database in a 'slow but more accurate' mode. So my questions: do you know how DOCK & AUTODOCK handle vHTS of large databases? Any personal experience or additional papers? Any one of these two programs is better than the other for vHTS? Thanks a lot in advance, Jerome Baudry UT/ORNL Center for Molecular Biophysics, Oak Ridge National Lab, TN. jerome- -scs.uiuc.edu