From owner-chemistry@ccl.net Thu Jan 19 00:57:00 2006 From: "SATOU Kazuhito katze(_)gsc.riken.jp" To: CCL Subject: CCL: Command-line tools for converting chemical files into graphics files? Message-Id: <-30567-060118210846-9482-JTPapeizhujmyRnoDBfJvA%a%server.ccl.net> X-Original-From: SATOU Kazuhito Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-2022-JP Date: Thu, 19 Jan 2006 10:08:36 +0900 MIME-Version: 1.0 Sent to CCL by: SATOU Kazuhito [katze%x%gsc.riken.jp] Hi there, Do you know any command-line tools for converting chemical files (.smi, .mol, ...) into graphics files (.jpg, .png, ...)? They must be free software (written in C/C++ are better) on Linux/Unix. The followings are proprietary :( 1. http://www.mol-net.de/software/image/ 2. http://www.acdlabs.com/products/glob_sol_lab/mol2gif/ 3. http://www.eyesopen.com/products/toolkits/ogham.html Thank you in advance. -- Visita Inferiora Terrae Rectificando Invenies Occultum Lapidem SATOU Kazuhito, Ph.D. Protein Function Team email: katze()gsc.riken.jp Protein Research Group phone: +81-45-503-9212 RIKEN Genomic Sciences Center fax : +81-45-503-9210 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan From owner-chemistry@ccl.net Thu Jan 19 03:23:00 2006 From: "Szabolcs Csepregi scsepregi^chemaxon.com" To: CCL Subject: CCL: Command-line tools for converting chemical files into graphics files? Message-Id: <-30568-060119032142-2496-WmjhO1gXdqcNI6R0gik6bw===server.ccl.net> X-Original-From: Szabolcs Csepregi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 19 Jan 2006 09:20:37 +0100 MIME-Version: 1.0 Sent to CCL by: Szabolcs Csepregi [scsepregi|a|chemaxon.com] Marvin's molconvert from ChemAxon is free if not used as part of an application. (Command line usage is certainly allowed.) It inputs most common molecular formats (mol, smiles, pdb, cml, etc.) and can generate images in various formats (jpg, bmp, png, ppm, svg) You can also save images directly from MarvinSketch (Also free if used as an application.) Description: http://www.chemaxon.com/marvin/doc/user/molconvert.html Download: http://www.chemaxon.com/marvin/download.html I hope that helps. Szabolcs --- Szabolcs Csepregi, PhD Cheminformatics Scientist, ChemAxon Ltd. http://www.chemaxon.com Skype: szabolcs.csepregi Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 SATOU Kazuhito katze(_)gsc.riken.jp wrote: > Sent to CCL by: SATOU Kazuhito [katze%x%gsc.riken.jp] > Hi there, > > Do you know any command-line tools for converting chemical files (.smi, > .mol, ...) into graphics files (.jpg, .png, ...)? They must be free > software (written in C/C++ are better) on Linux/Unix. > > The followings are proprietary :( > 1. http://www.mol-net.de/software/image/ > 2. http://www.acdlabs.com/products/glob_sol_lab/mol2gif/ > 3. http://www.eyesopen.com/products/toolkits/ogham.html > > Thank you in advance. > From owner-chemistry@ccl.net Thu Jan 19 04:56:01 2006 From: "Jamie Platts platts],[Cardiff.ac.uk" To: CCL Subject: CCL: pi-stacking in ligand-protein interactions Message-Id: <-30569-060119045327-20607-HXerKBiV3iM/d7r9fmxGPg[a]server.ccl.net> X-Original-From: "Jamie Platts" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 19 Jan 2006 09:12:21 +0000 Mime-Version: 1.0 Sent to CCL by: "Jamie Platts" [platts.^-^.Cardiff.ac.uk] Dear Christian There's a very nice paper by Sinnokrot & Sherrill which shows that substituted benzenes in the stacked "parallel displaced" conformation have stronger binding than the benzene dimer itself. Interestingly, this is the case whether the substituent is electron withdrawing (-F, -CN) or donating (-OH, -CH3). Substituent Effects in pi-pi Interactions: Sandwich and T-Shaped Configurations Mutasem Omar Sinnokrot and C. David Sherrill J. AM. CHEM. SOC. 2004, 126, 7690-7697. We have also done some work which suggests that pyridine- benzene is slightly more strongly bound than benzene-benzen (due out in J Comp Chem soon). Hope this helps, Jamie ---------------------------------------------------------- Jamie Platts School of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts^-^cf.ac.uk Park Place FAX: +44 (0) 2920 874030 Cardiff CF10 3AT www.cf.ac.uk/chemy >>> owner-chemistry^-^ccl.net 01/18/06 10:02 pm >>> Sent to CCL by: christian.pilger{:}basf.com Dear CCLers, in one of my projects, I'm dealing with a protein that contains two phenylalanins oriented in such way that their phenylrings parallel each other. Between these two phenyl rings there is enough space to hold a ligand pi-system. My question: does it make a difference whether the ligand pi-system is electron rich (e.g. thiophen, pyrrole, indole etc.) or electron poor (pyridine, nitrobenzene etc.) ? Can a distinction be made, which type of pi-system would contribute more to ligand binding ? I can imagine, that in case the two phenylalanines were replaced by more electron rich tyrosines, an electron poor ligand pi-system could be advantegous because two electron rich system would repulse each other. Has anybody been concerned with this problem ? Are there references available in the literature that discuss this matter ? Any comments are welcome. Thanks in advance. Best regards, Christian _____________________________________________________________________________ BASF - Global Research Agricultural Products, GVA / FI E-Mail: christian.pilger=basf.com Postal Address: BASF Aktiengesellschaft, Ludwigshafen, D-67056, Ludwigshafen, Germany From owner-chemistry@ccl.net Thu Jan 19 05:31:00 2006 From: "Peter Waaben Thulstrup pwt_-_kvl.dk" To: CCL Subject: CCL: Summary on "Systematic DFT study of spin states for (first row transition metal) coordination compou Message-Id: <-30570-060119045650-21561-T6e7N3FE/I0xmQSJ/bwuvg-.-server.ccl.net> X-Original-From: "Peter Waaben Thulstrup" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=Windows-1252 Date: Thu, 19 Jan 2006 10:56:28 +0100 Mime-Version: 1.0 Sent to CCL by: "Peter Waaben Thulstrup" [pwt[-]kvl.dk] Hello CCL, I received many useful responses to my enquiry regarding systematic studies of the reliability of DFT for prediction of spin states for coordination compounds. I would like to thank all those who took time to help me get an overview of this important area. I have included all the references below (anonymized and in random order): M. Swart, A.R. Groenhof, A.W. Ehlers and K. Lammertsma "Validation of exchange-correlation functionals for spin states of iron-complexes" J. Phys. Chem. A 2004, 108, 5479-5483 - Deeth et al J. Comput. Chem. 2004,25,1840 Harvey, J. N. Structure and Bonding 2004,112,151 Slomon et al, J. Chem. Phys. 2002,117,4729 Reiher et al, Theor. Chem. Acc. 2001,107,48 The Structure and Bonding article is an extremely good review for the deltaSCF approach. A very recent methodology called spin-flipping TDDFT is available in the ADF package. The relevant articles are: Wang, F. Ziegler, T. J. Chem. Phys. 2005,122,074109 Seth, M. Ziegler, T. J. Chem Phys. 2005,123,144105 The latter attempts to alleviate the problem of the multi-reference character and degeneracies in transition metal complexes. - For a particular case (not a systematic study), take a look at the following reference: J. Poater, M. Solà, A. Rimola, L. Rodríguez-Santiago and M. Sodupe J. Phys. Chem. A, 108 (2004) 6072-6078. - Have a look to papers published by Holthausen M. C. and Koch W. - Fouqeau, A.; Casida, M.E.; Lawson, L.M.; Hauser, A.; Neese, F. (2005) Comparison of Density Functionals for Energy and Structural Differences Between the High-[5T2g: (t2g4)(eg2)] and Low-[1A1g: (t2g6)(eg0)] Spin States of Iron(II) Coordination Compounds : II. Comparison of Results for More than Ten Modern Functionals with Ligand Field Theory and Ab Initio Results for Hexaquoferrous Dication, [Fe(H2O)6]2+ and Hexaminoferrous Dication [Fe(NH3)6]2+, J. Chem. Phys., 122, 044110/1-13 Fouqueau, A.; Mer, S.; Casida, M.E.; Daku, L.M.L.; Hauser, A.; Mieva, T.; Neese, F. (2004) Comparison of Density Functionals for Energy and Structural Differences between the High [5T2g: t2g4eg2] and Low [1A1g: t2g6] Spin States of the Hexaquo-Ferrous Ion, [Fe(H2O)6]2+, J. Chem. Phys., 120, 9473-9486. Schöneboom, J.; Neese, F.; Thiel, W. (2005) Towards Identification of the Compound I Reactive Intermediate in Cytochrome P450 Chemistry: A QM/MM Study of its EPR and Mössbauer Parameters, J. Am. Chem. Soc., 127, 5840-5853 and references therein. There have been quite a few studies. DFT tends to be biased in favour of low spin states. - Best regards, Peter W. Thulstrup - Assistant Professor Peter W. Thulstrup, Ph.D. Bioinorganic Chemistry Group, Department of Natural Sciences The Royal Veterinary and Agricultural University Thorvaldsensvej 40 - DK-1871 Frederiksberg - Denmark Phone: +45 35282464 - Fax: +45 35282398 - Mobile: +45 40550527 E-mail: pwt.:.kvl.dk - Web: http://www.natsci.kvl.dk/~pwt From owner-chemistry@ccl.net Thu Jan 19 06:06:01 2006 From: "Noel O Boyle no228() cam.ac.uk" To: CCL Subject: CCL: Command-line tools for converting chemical files into graphics files? Message-Id: <-30571-060119050027-24279-zFSMSXi5lueLT8kpUE89Cw() server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 19 Jan 2006 10:00:16 +0000 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [no228],[cam.ac.uk] On Thu, 2006-01-19 at 01:02 -0500, SATOU Kazuhito katze(_)gsc.riken.jp wrote: > Sent to CCL by: SATOU Kazuhito [katze%x%gsc.riken.jp] > Hi there, > > Do you know any command-line tools for converting chemical files (.smi, > .mol, ...) into graphics files (.jpg, .png, ...)? They must be free > software (written in C/C++ are better) on Linux/Unix. > > The followings are proprietary :( Do you mean free as in no price, or free as in non-proprietary (i.e. Open Source)? Regards, Noel From owner-chemistry@ccl.net Thu Jan 19 07:50:00 2006 From: "Pierre Mignon pmignon\a/vub.ac.be" To: CCL Subject: CCL: pi-stacking in ligand-protein interactions Message-Id: <-30572-060119070230-22971-XS9ZZdKgX045BGT2mR9KbA,,server.ccl.net> X-Original-From: Pierre Mignon Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1" Date: Thu, 19 Jan 2006 12:08:03 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Pierre Mignon [pmignon(-)vub.ac.be] Dear, The fact that the pi-system is electron-rich or electron-poor has an effect on the different contributions to the stabilization energy: electrostatics and dispersion. On one hand if the system is electron rich you will have a larger electrostatis repulsion between the cycles, on the other hand it may have a effect on the polarizability of the considered system and then on the disperion energy which is the cause of stabilization of stacked pi-systems. For a references, you can take a look to: Influence of Stacking on Hydrogen Bonding: Quantum Chemical Study on Pyridine-Benzene Model Complexes. Pierre Mignon, Stefan Loverix, Frank De Proft, Paul Geerlings. Journal of Physical Chemistry A 2004, 108, 6038-6044. Influence of the pi-pi Interaction on the Hydrogen Bonding Capacity of Stacked DNA/RNA Bases. Pierre Mignon, Stefan Loverix, Jan Steyaert, Paul Geerlings. Nucleic Acids Research, 2005, 33, 1779-1789. In contrast to the studies of sinnokrot, the cited references above, study the different contributions to the staking energy for much more subsituted benzenes (10) and show that the electrostatic contribution depends on the electron donating/accepting character of the substituent, it is shown by using DFT based descriptors. One 'bémol' to our conclusion would be: the tendancy is more clear for electron withdrawing substituents. bye, Pierre. >Sent to CCL by: "Jamie Platts" [platts.[].Cardiff.ac.uk] >Dear Christian > >There's a very nice paper by Sinnokrot & Sherrill which shows >that substituted benzenes in the stacked "parallel displaced" >conformation have stronger binding than the benzene dimer >itself. Interestingly, this is the case whether the substituent >is electron withdrawing (-F, -CN) or donating (-OH, -CH3). > >Substituent Effects in pi-pi Interactions: Sandwich and T-Shaped >Configurations >Mutasem Omar Sinnokrot and C. David Sherrill >J. AM. CHEM. SOC. 2004, 126, 7690-7697. > >We have also done some work which suggests that pyridine- >benzene is slightly more strongly bound than benzene-benzen >(due out in J Comp Chem soon). > >Hope this helps, > >Jamie > >---------------------------------------------------------- > Jamie Platts > School of Chemistry Phone: +44 (0) 2920 874950 > Cardiff University Email: platts/a\cf.ac.uk > Park Place FAX: +44 (0) 2920 874030 > Cardiff CF10 3AT www.cf.ac.uk/chemy > >>>> owner-chemistry/a\ccl.net 01/18/06 10:02 pm >>> >Sent to CCL by: christian.pilger{:}basf.com >Dear CCLers, > >in one of my projects, I'm dealing with a protein that contains two >phenylalanins oriented in such way that their phenylrings parallel each >other. Between these two phenyl rings there is enough space to hold a >ligand pi-system. My question: does it make a difference whether the ligand >pi-system is electron rich (e.g. thiophen, pyrrole, indole etc.) or >electron poor (pyridine, nitrobenzene etc.) ? Can a distinction be made, >which type of pi-system would contribute more to ligand binding ? I can >imagine, that in case the two phenylalanines were replaced by more electron >rich tyrosines, an electron poor ligand pi-system could be advantegous >because two electron rich system would repulse each other. Has anybody been >concerned with this problem ? Are there references available in the >literature that discuss this matter ? > >Any comments are welcome. Thanks in advance. > >Best regards, > >Christian > >_____________________________________________________________________________ > >BASF - Global Research Agricultural Products, GVA / FI > > >E-Mail: christian.pilger=basf.com >Postal Address: BASF Aktiengesellschaft, Ludwigshafen, D-67056, >Ludwigshafen, Germany> > > > Mignon Pierre PhD Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 35 80 Fax + 32 2 629 33 17 e-mail pmignon[]vub.ac.be From owner-chemistry@ccl.net Thu Jan 19 09:28:00 2006 From: "Dr. Seth Olsen s.olsen1()uq.edu.au" To: CCL Subject: CCL: Command-line tools for converting chemical files into graphics files? Message-Id: <-30573-060119031049-596-3r3KwIhMrNa76QU7agVLTA===server.ccl.net> X-Original-From: "Dr. Seth Olsen" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 19 Jan 2006 18:10:40 +1000 MIME-Version: 1.0 Sent to CCL by: "Dr. Seth Olsen" [s.olsen1|a|uq.edu.au] OpenBabel. SATOU Kazuhito katze(_)gsc.riken.jp wrote: >Sent to CCL by: SATOU Kazuhito [katze%x%gsc.riken.jp] >Hi there, > >Do you know any command-line tools for converting chemical files (.smi, >.mol, ...) into graphics files (.jpg, .png, ...)? They must be free >software (written in C/C++ are better) on Linux/Unix. > >The followings are proprietary :( >1. http://www.mol-net.de/software/image/ >2. http://www.acdlabs.com/products/glob_sol_lab/mol2gif/ >3. http://www.eyesopen.com/products/toolkits/ogham.html > >Thank you in advance. > > From owner-chemistry@ccl.net Thu Jan 19 10:03:00 2006 From: "JAMES VIVIAN jamestvivian\a/msn.com" To: CCL Subject: CCL: Multiscale fluorescence simulation studies? Message-Id: <-30574-060119083335-18236-xt2b6gGambsU7Ol4u7hnwQ _ server.ccl.net> X-Original-From: "JAMES VIVIAN" Content-Type: text/plain; format=flowed Date: Thu, 19 Jan 2006 08:33:23 -0500 Mime-Version: 1.0 Sent to CCL by: "JAMES VIVIAN" [jamestvivian*msn.com] Seth: Here's a starting point: http://www.chemistry.montana.edu/callis.html/ Contains a handful of publication links; references therein provide a pretty good overview/roadmap. Best, Jim >From: "Dr Seth Olsen s.olsen1{:}uq.edu.au" >Reply-To: "CCL Subscribers" >To: "Vivian, James T " >Subject: CCL: Multiscale fluorescence simulation studies? >Date: Wed, 18 Jan 2006 22:37:06 -0500 > >Sent to CCL by: Dr Seth Olsen [s.olsen1_-_uq.edu.au] > > >Hi CCL'ers, > >I've been trying to chase up references that describe attempts to >perform excited state dynamics on timescales relevant to fluorescence >lifetimes. As someone with a background in ab initio excited state >calculations and excited state dynamics simulations, I am quite aware >that a straightforward excited state dynamics simulation on the >nanoseconds to tens of nanoseconds timescale may be a bit of a >challenge. What I'm interested in are questions of how the excited >state potential surface changes the conformations sampled on the >relevant timescale. I'm particularly interested in the case of a >fluorophore bound to a protein. I've done some current contents >searches, searches in relevant journals and googled it. I've found some >items but it's not clear that its the sort of thing I'm looking for - >namely a legitimate atomistic description of the stokes shift in a >protein based (at the foundation) in first principles, that attempts to >characterize timescales and possibly temperature dependencies of the >stokes shift and the fluorescence spectral envelope. > >If anyone knows of any good references that they think may fit the bill, >I'd be happy to receive them. > >Cheers, > >Seth > > >ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > >Dr Seth Olsen, PhD >Postdoctoral Fellow, Biomolecular Modeling Group >Centre for Computational Molecular Science >Chemistry Building, >The University of Queensland >Qld 4072, Brisbane, Australia > >tel (617) 33653732 >fax (617) 33654623 >email: s.olsen1[#]uq.edu.au >Web: www.ccms.uq.edu.au > >ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms> > > From owner-chemistry@ccl.net Thu Jan 19 10:38:00 2006 From: "Paul Hawkins phawkins^-^eyesopen.com" To: CCL Subject: CCL: Command-line tools for converting chemical files into graphics files? Message-Id: <-30575-060119022025-29084-HT3IpxE/RrOiBdFIqoQQeA . server.ccl.net> X-Original-From: Paul Hawkins Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 18 Jan 2006 23:35:37 -0700 MIME-Version: 1.0 Sent to CCL by: Paul Hawkins [phawkins#,#eyesopen.com] Dear Satuo, If your research is academic then the OGHAM toolkit is free. OpenEye only charges commercial customers or those intending to use our tools to make products. If your purpose is research only then all the OpenEye tools are free of charge. Paul. Paul Hawkins Senior Applications Scientist OpenEye Scientific Software SATOU Kazuhito katze(_)gsc.riken.jp wrote: >Sent to CCL by: SATOU Kazuhito [katze%x%gsc.riken.jp] >Hi there, > >Do you know any command-line tools for converting chemical files (.smi, >.mol, ...) into graphics files (.jpg, .png, ...)? They must be free >software (written in C/C++ are better) on Linux/Unix. > >The followings are proprietary :( >1. http://www.mol-net.de/software/image/ >2. http://www.acdlabs.com/products/glob_sol_lab/mol2gif/ >3. http://www.eyesopen.com/products/toolkits/ogham.html > >Thank you in advance. > > From owner-chemistry@ccl.net Thu Jan 19 11:13:01 2006 From: "Roman D. Gorbunov gorbunov^theochem.uni-frankfurt.de" To: CCL Subject: CCL:G: Dipole moment with Gaussian. Message-Id: <-30576-060119093236-27835-ALyIErVk+R1PnUcRnOFAgw_-_server.ccl.net> X-Original-From: "Roman D. Gorbunov" Sent to CCL by: "Roman D. Gorbunov" [gorbunov*theochem.uni-frankfurt.de] Thanks a lot. I checked everything. The second dipole (written after "Test job not archived") is really given in the input-orientation frame and in atomic units. While the first vector is given in standard-orientation frame and in Debyes. Thank you. > The archived data give the dipole moment in atomic units. > The length of this vector is sqrt[(1.203..)^2+(-.945..)^2+(.473..)^2] > = 1.60164 a.u. which is the same thing as 4.071 Debye. > The orientation is probably that of the original molecule -- > Gaussian re-orients your molecule to a "standard oreintation" > before doing any calculations, and the Dip Moment in Debye > refers to the standard orientation. From owner-chemistry@ccl.net Thu Jan 19 11:47:01 2006 From: "Roman D. Gorbunov gorbunov]=[theochem.uni-frankfurt.de" To: CCL Subject: CCL:G: Transition Dipole Moment with Gaussian. Message-Id: <-30577-060119104553-19328-TNnFDgQi2k9KpBXwgExo1A|a|server.ccl.net> X-Original-From: "Roman D. Gorbunov" Sent to CCL by: "Roman D. Gorbunov" [gorbunov%theochem.uni-frankfurt.de] Dear All, I would like to calculate transition dipole moment of a molecule with the usage of Gaussian program. If Gaussian calculate normal modes, in the end of the output files one can find something like this: MSD=1.034e-09\RMSF=5.113e-05\Dipole=1.203046,-0.9454618,0.4733203\Dipo leDeriv=0.3104709,0.0526555,-0.0901773,0.0975203,0.3147646,-0.1101542, -0.1478299,-0.0861128,0.4431087,-1.1332275,0.0824717,0.2775604,0.07129 I supposed that numbers coming after DipoleDeriv are derivatives of the dipole moment over normal coordinates (i. e. transition dipole moments). I also supposed that they are given in the initial-orientation frame (just like the dipole moment vector coming right before). However, under this suppositions I cannot get expected results. Does anybody know the exact definition and printing format of the dipole derivatives tensor in Gaussian output files? Or may be where one can read about that? Thank you in advance. From owner-chemistry@ccl.net Thu Jan 19 12:22:00 2006 From: "T. Daniel Crawford crawdad!=!exchange.vt.edu" To: CCL Subject: CCL:G: Transition Dipole Moment with Gaussian. Message-Id: <-30578-060119121920-2687-iO8cLnG6ux/9JuowSpJXoQ(~)server.ccl.net> X-Original-From: "T. Daniel Crawford" Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Thu, 19 Jan 2006 12:19:12 -0500 Mime-version: 1.0 Sent to CCL by: "T. Daniel Crawford" [crawdad*exchange.vt.edu] Roman, I think it is more likely that the dipole moment derivatives are given with respect to Cartesian coordinates in the original frame and in atomic units (just as for the dipole moments). These can be transformed to the normal coordinate representation and subsequently used for computing infrared intensities, for example. -Daniel On 1/19/06 12:01 PM, "Roman D. Gorbunov gorbunov]=[theochem.uni-frankfurt.de" wrote: > Sent to CCL by: "Roman D. Gorbunov" [gorbunov%theochem.uni-frankfurt.de] > Dear All, > > I would like to calculate transition dipole moment of a molecule with the > usage of Gaussian program. If Gaussian calculate normal modes, in the end of > the output files one can find something like this: > > MSD=1.034e-09\RMSF=5.113e-05\Dipole=1.203046,-0.9454618,0.4733203\Dipo > leDeriv=0.3104709,0.0526555,-0.0901773,0.0975203,0.3147646,-0.1101542, > -0.1478299,-0.0861128,0.4431087,-1.1332275,0.0824717,0.2775604,0.07129 > > I supposed that numbers coming after DipoleDeriv are derivatives of the dipole > moment over normal coordinates (i. e. transition dipole moments). I also > supposed that they are given in the initial-orientation frame (just like the > dipole moment vector coming right before). However, under this suppositions I > cannot get expected results. Does anybody know the exact definition and > printing format of the dipole derivatives tensor in Gaussian output files? Or > may be where one can read about that? > > Thank you in advance.> > > -- 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 Thu Jan 19 13:00:00 2006 From: "Rajarshi Guha rxg218(a)psu.edu" To: CCL Subject: CCL: Command-line tools for converting chemical files into graphics files? Message-Id: <-30579-060119103238-13349-US07bTqC0sLcLFA0Qci7hA]*[server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 19 Jan 2006 08:42:03 -0500 Mime-Version: 1.0 Sent to CCL by: Rajarshi Guha [rxg218=psu.edu] On Thu, 2006-01-19 at 01:08 -0500, SATOU Kazuhito katze(_)gsc.riken.jp wrote: > Sent to CCL by: SATOU Kazuhito [katze%x%gsc.riken.jp] > Hi there, > > Do you know any command-line tools for converting chemical files (.smi, > .mol, ...) into graphics files (.jpg, .png, ...)? They must be free > software (written in C/C++ are better) on Linux/Unix. http://blue.chem.psu.edu/~rajarshi/code/java/#draw2d - uses the CDK to generate PNG or JPEG's from SDF's ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- "A fractal is by definition a set for which the Hausdorff Besicovitch dimension strictly exceeds the topological dimension." -- Mandelbrot, "The Fractal Geometry of Nature" From owner-chemistry@ccl.net Thu Jan 19 13:35:00 2006 From: "Nuno R. L. Ferreira nunolf~!~ci.uc.pt" To: CCL Subject: CCL: Synthesize X-ray pattern Message-Id: <-30580-060119124812-29207-TJjCMeq95SrxTDE3rSAUpg[*]server.ccl.net> X-Original-From: "Nuno R. L. Ferreira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 19 Jan 2006 16:37:15 -0000 MIME-Version: 1.0 Sent to CCL by: "Nuno R. L. Ferreira" [nunolf],[ci.uc.pt] Hi * I'm looking for a free tool that syntesizes the X-ray pattern, given a protein pdb file. Best regards, Nuno ###################################### Nuno Ricardo Santos Loureiro da Silva Ferreira Departamento de Química Faculdade de Ciências e Tecnologia Universidade de Coimbra 3004-535 Coimbra - Portugal Fax: +351 239 827703 - www.biolchem.qui.uc.pt ######################################## --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0603-3, 18-01-2006 Tested on: 19-01-2006 16:37:16 avast! - copyright (c) 1988-2005 ALWIL Software. http://www.avast.com From owner-chemistry@ccl.net Thu Jan 19 14:10:01 2006 From: "Egon Willighagen egonw===sci.kun.nl" To: CCL Subject: CCL: Command-line tools for converting chemical files into graphics files? Message-Id: <-30581-060119135015-7296-8pF/qKXZfvpkajLefYGJIg:+:server.ccl.net> X-Original-From: Egon Willighagen Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Thu, 19 Jan 2006 19:50:01 +0100 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egonw###sci.kun.nl] On Thursday 19 January 2006 19:19, Rajarshi Guha rxg218(a)psu.edu wrote: > Sent to CCL by: Rajarshi Guha [rxg218=psu.edu] > On Thu, 2006-01-19 at 01:08 -0500, SATOU Kazuhito katze(_)gsc.riken.jp > > Sent to CCL by: SATOU Kazuhito [katze%x%gsc.riken.jp] > > Do you know any command-line tools for converting chemical files (.smi, > > .mol, ...) into graphics files (.jpg, .png, ...)? They must be free > > software (written in C/C++ are better) on Linux/Unix. > > http://blue.chem.psu.edu/~rajarshi/code/java/#draw2d - uses the CDK to > generate PNG or JPEG's from SDF's And what about converting a SDF into 2D graphics wrapped into a PDF? Are there free or open source tools for that too? Egon -- e.willighagen~!~science.ru.nl PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen Blog: http://chem-bla-ics.blogspot.com/ http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 From owner-chemistry@ccl.net Thu Jan 19 15:06:00 2006 From: "janl]^[speakeasy.net" To: CCL Subject: CCL: Command-line tools for converting chemical files into graphics files? Message-Id: <-30582-060119150252-21688-5EvX2NUUqLaAoDv/Z6NmZw-.-server.ccl.net> X-Original-From: janl(0)speakeasy.net Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 19 Jan 2006 20:02:44 +0000 MIME-Version: 1.0 Sent to CCL by: janl!^!speakeasy.net > -----Original Message----- > From: Rajarshi Guha rxg218(a)psu.edu [mailto:owner-chemistry::ccl.net] > Sent: Thursday, January 19, 2006 06:24 PM > To: 'Labanowski, Jan ' > Subject: CCL: Command-line tools for converting chemical files into graphics files? > > http://blue.chem.psu.edu/~rajarshi/code/java/#draw2d - uses the CDK to > generate PNG or JPEG's from SDF's > And once you have PNG, JPEG, JPG, GIF you can easily convert them to PS (PostScript) or Encapsulated Postscript by using GIMP (automatically installed on most Linux Systems -- just read it as, say fig.gif and save it as fig.ps or fig.eps) http://www.gimp.org (also available for Windoz) You can also use ImageMagick tools to convert picture format files: http://www.cit.gu.edu.au/~anthony/graphics/imagick6/ and create pictures and logos from the command line: for example: convert fig.gif fig.ps or convert fig.gif fig.eps and once you have a postscript, you can always convert it to PDF by simple: ps2pdf fig.ps fig.pdf on most linux systems and if you have to have to use Windows, get and install Cygwin http://www.cygwin.com that has most of these goodies included (but you have to tell it to install it by selecting them during setup -- click on graphics tools and select them). From my humble perspective, having Cygwin on your windows is a MUST -- many Linux goodies and X-Windows, and ssh, and compilers and more...). CYgwin instals by itself and works great... Just another plug for Open Software... Jan From owner-chemistry@ccl.net Thu Jan 19 15:40:01 2006 From: "David van der Spoel spoel/./xray.bmc.uu.se" To: CCL Subject: CCL: Synthesize X-ray pattern Message-Id: <-30583-060119153227-7264-VB1IWMwKp9CaTN+XfQazMg::server.ccl.net> X-Original-From: David van der Spoel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 19 Jan 2006 20:49:59 +0100 MIME-Version: 1.0 Sent to CCL by: David van der Spoel [spoel%xray.bmc.uu.se] Nuno R. L. Ferreira nunolf~!~ci.uc.pt wrote: > Sent to CCL by: "Nuno R. L. Ferreira" [nunolf],[ci.uc.pt] > Hi * > > I'm looking for a free tool that syntesizes the X-ray pattern, given a > protein pdb file. > Best regards, check CCP4 programs. > Nuno > > ###################################### > Nuno Ricardo Santos Loureiro da Silva Ferreira > Departamento de Química > Faculdade de Ciências e Tecnologia > Universidade de Coimbra > 3004-535 Coimbra - Portugal > Fax: +351 239 827703 - www.biolchem.qui.uc.pt > ######################################## > > > > --- > avast! Antivirus: Outbound message clean. > Virus Database (VPS): 0603-3, 18-01-2006 > Tested on: 19-01-2006 16:37:16 > avast! - copyright (c) 1988-2005 ALWIL Software. > http://www.avast.com> > -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel*o*xray.bmc.uu.se spoel*o*gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-chemistry@ccl.net Thu Jan 19 16:15:00 2006 From: "Rajarshi Guha rxg218 : psu.edu" To: CCL Subject: CCL: Command-line tools for converting chemical files into graphics files? Message-Id: <-30584-060119155419-15746-O1flqmxHVVNezk+9F0fIZw+/-server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 19 Jan 2006 15:54:41 -0500 Mime-Version: 1.0 Sent to CCL by: Rajarshi Guha [rxg218[*]psu.edu] On Thu, 2006-01-19 at 14:18 -0500, Egon Willighagen egonw===sci.kun.nl wrote: > Sent to CCL by: Egon Willighagen [egonw###sci.kun.nl] > On Thursday 19 January 2006 19:19, Rajarshi Guha rxg218(a)psu.edu wrote: > > Sent to CCL by: Rajarshi Guha [rxg218=psu.edu] > > On Thu, 2006-01-19 at 01:08 -0500, SATOU Kazuhito katze(_)gsc.riken.jp > > > Sent to CCL by: SATOU Kazuhito [katze%x%gsc.riken.jp] > > > Do you know any command-line tools for converting chemical files (.smi, > > > .mol, ...) into graphics files (.jpg, .png, ...)? They must be free > > > software (written in C/C++ are better) on Linux/Unix. > > > > http://blue.chem.psu.edu/~rajarshi/code/java/#draw2d - uses the CDK to > > generate PNG or JPEG's from SDF's > > And what about converting a SDF into 2D graphics wrapped into a PDF? Are there > free or open source tools for that too? The program is now updated to optionally produce PDF output. It needs the iText library ( http://www.lowagie.com/iText/index.html ) to be in the CLASSPATH. Latest version can be obtained from http://blue.chem.psu.edu/~rajarshi/code/java/#draw2d ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- How I wish I were what I was when I wished I were what I am. From owner-chemistry@ccl.net Thu Jan 19 20:25:00 2006 From: "Warren DeLano warren,,delsci.com" To: CCL Subject: CCL: Program or Script to Calculate Atom-Atom Distances in pdb files Message-Id: <-30585-060119202341-17862-fqYhtlRl75UgUodW6isi9w]^[server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 Jan 2006 17:25:29 -0800 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren a delsci.com] Irida, > I am looking for a free program > or script that can calculate all sulfur-sulfur distances in > pdb files from the Protein Data Bank. This is the kind of problem you can solve in PyMOL with just a few lines of Python code. For example: > from pymol import cmd > from glob import glob for file in glob("*.pdb"): print file cmd.load(file,'prot') for a in cmd.index("elem s and bound_to elem s"): if cmd.select("s1","%s`%d"%a) and \ cmd.select("s2","elem s and bound_to %s`%d"%a): if cmd.select("(s1|s2) and not ?skip"): cmd.iterate("s1|s2","print ' ',chain,resn,resi,name") print ' ',round(cmd.dist("tmp","s1","s2"),3) cmd.select("skip","s1|s2|?skip") cmd.delete("all") Would generate the following output in a directory with pdb files: 1alk.pdb A CYS 168 SG A CYS 178 SG 1.975 A CYS 286 SG A CYS 336 SG 1.995 B CYS 168 SG B CYS 178 SG 1.996 B CYS 286 SG B CYS 336 SG 2.032 1btu.pdb CYS 42 SG CYS 58 SG 2.039 CYS 136 SG CYS 201 SG 2.031 CYS 168 SG CYS 182 SG 2.001 CYS 191 SG CYS 220 SG 2.019 ... Note that the above is for bonded sulfurs in disulfides. For all intra-cysteine gamma sulfur distances, you'd want to do something more like: > from pymol import cmd > from glob import glob for file in glob("*.pdb"): print file cmd.load(file,'prot') for a in cmd.index("CYS/SG"): for b in cmd.index("CYS/SG"): if a[1] -----Original Message----- > From: owner-chemistry{}ccl.net [mailto:owner-chemistry{}ccl.net] > Sent: Wednesday, January 18, 2006 6:03 PM > To: Warren DeLano > Subject: CCL: Program or Script to Calculate Atom-Atom > Distances in pdb files > > Sent to CCL by: "Irida Kastrati" [ikastr2[a]uic.edu] > Hello CCLers, > Because of some excellent feedback I received when I asked > for help about a year ago, I thought of using the CCL members > expertise again this time. I am looking for a free program > or script that can calculate all sulfur-sulfur distances in > pdb files from the Protein Data Bank. The program or script > should be able to read the massive database of protein > structures from the Protein Data Bank, or a local copy of PDB > files. Then, pinpoint S-S distances within a certain value, > or calculate the actual distance. I have access to SYBYL. > Any suggestion is very welcome! > Thank you in advance for your time and help. > > Sincerely, > Irida Kastrati > e-mail: ikastr2{=}uic.edu > University of IL at Chicago > College of Pharmacy, Medicinal Chemistry > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > >