From owner-chemistry@ccl.net Mon Feb 22 01:47:00 2010 From: "Alexander Bagaturyants sasha .. photonics.ru" To: CCL Subject: CCL:G: G03 Temperature Parameter Message-Id: <-41309-100222013024-20321-JU78qJ+Oc2NfKQXR8nUM1Q%server.ccl.net> X-Original-From: "Alexander Bagaturyants" Content-Language: ru Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" Date: Mon, 22 Feb 2010 09:30:09 +0300 MIME-Version: 1.0 Sent to CCL by: "Alexander Bagaturyants" [sasha:-:photonics.ru] Finally, we have got a correct answer to the question after some = misleading comments. There is an evident difference between quantum-mechanical values, which refer to a certain quantum-mechanical state, and thermodynamic values, = which refer to a thermodynamic ensemble (or, for an isothermal process, to a certain temperature). These simple statements must be known to any = student or novice researcher in quantum chemistry or molecular simulations.=20 However, this is so trivial that hardly deserves a discussion, and you should not be an expert to understand that. Prof. Alexander A. Bagatur'yants Photochemistry Center Russian Academy of Sciences ul. Novatorov 7a Moscow 119421 Russia Phone: +7(495)9362588 (office) +7(916)5317022 (mobile) Fax: +7(495)9361255 e-mail: sasha|-|photonics.ru=20 bagaturyants|-|gmail.com > From: owner-chemistry+sasha=3D=3Dphotonics.ru|-|ccl.net [mailto:owner-chemistry+sasha=3D=3Dphotonics.ru|-|ccl.net] On Behalf Of = Marcel Swart marcel.swart ~~ icrea.es Sent: Monday, February 22, 2010 1:08 AM To: Bagaturyants, Alexander A. Subject: CCL: G03 Temperature Parameter In any quantum-chemistry program, the temperature one can set on input = has effect mainly on the thermodynamic analysis, i.e. how the vibrational frequencies can = be transformed into enthalpy, entropy and free energy. The electronic energy, HOMO, LUMO, optimization, etc. are completely independent of the temperature.=A0 Please read a good introductory textbook like Jensen's "Introduction to computational=A0chemistry", or any one of the introductory textbooks (Szabo/Ostlund, McWeeny, Leach, Cramer, etc.). =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart*|*icrea.es marcel.swart*|*udg.edu web http://www.marcelswart.eu =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From owner-chemistry@ccl.net Mon Feb 22 03:20:00 2010 From: "Andreas Klamt klamt(_)cosmologic.de" To: CCL Subject: CCL: Estimation of viscosity from molecular weight Message-Id: <-41310-100221134039-2834-QTSK6M3f/1F8NgNs+FMNPg|*|server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Sun, 21 Feb 2010 19:40:22 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt^^cosmologic.de] Hi Alex, while admittedly I do not understand what David wants to say with his comment, my entry was serious. COSMOtherm allows you to calculate viscosity just from the structure of the compound, based on the ideas which I described in my previous messages. Hence it exactly does what you are looking for. Andreas Alex Naden anaden{=}fsmail.net schrieb: > Sent to CCL by: "Alex Naden" [anaden{:}fsmail.net] > Hi guys, > > I am not sure where my question is going but it somehow does not look like a right direction... I need to explain the differences in a diffusion zone of some liquids on a solid surface, so my first idea was to look at the differences in their viscosities. As the only data that I have for the compounds was the molecular weight and their structure my idea was to estimate viscosities (if possible). If there are any useful suggestions on the subject they will be VERY welcome. > > Thank you, > > Alex> > > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt]~[cosmologic.de web www.cosmologic.de HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Mon Feb 22 03:54:01 2010 From: "Soren Eustis soreneustis/a\gmail.com" To: CCL Subject: CCL:G: G03 Temperature Parameter Message-Id: <-41311-100222032550-24752-/RtqatJBymwQ3dQICeI8qA,+,server.ccl.net> X-Original-From: Soren Eustis Content-transfer-encoding: quoted-printable Content-type: text/plain; charset="ISO-8859-1" Date: Mon, 22 Feb 2010 09:25:34 +0100 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis*|*gmail.com] Agreed. His question was improperly formed and thus fatally flawed. I understood that, and I believe most of us reading it understood it as well. Gaussian, and many other codes, allows you to input T and P values for thermodynamic analysis. I was giving the poster the benefit of the doubt that he realized he understood this was a thermodynamic (ensemble), rather than quantum mechanical property. The crux of his question was that he needed to know how to enter T into his calculations. When someone posts to the board looking for help, I think we should give them that whenever possible, and always avoid condescension. Perhaps the correct response was a combination of all that were given. example: you can enter temperature and pressure into Gaussian calculations via the temperature and pressure keywords (see: http://www.gaussian.com/g_tech/g_ur/l_keywords09.htm). Yet, be aware that these are ensemble properties and not quantum mechanical ones. Thus, make sure that the variable you are choosing is applicable to your problem. For more information, see the Gaussian white paper on Thermochemistry ( http://www.gaussian.com/g_whitepap/thermo.htm) Regards, Soren --=20 Dr. Soren N. Eustis ETH =AD Zurich Institute for Biogeochemistry and Pollutant Dynamics Universitatstrasse 16 8092 Zurich +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren=env.ethz.ch On 2/22/10 7:30 AM, "Alexander Bagaturyants sasha .. photonics.ru" wrote: >=20 > Sent to CCL by: "Alexander Bagaturyants" [sasha:-:photonics.ru] > Finally, we have got a correct answer to the question after some misleadi= ng > comments. > There is an evident difference between quantum-mechanical values, which > refer to a certain quantum-mechanical state, and thermodynamic values, wh= ich > refer to a thermodynamic ensemble (or, for an isothermal process, to a > certain temperature). These simple statements must be known to any studen= t > or novice researcher in quantum chemistry or molecular simulations. > However, this is so trivial that hardly deserves a discussion, and you > should not be an expert to understand that. >=20 > Prof. Alexander A. Bagatur'yants > Photochemistry Center > Russian Academy of Sciences > ul. Novatorov 7a > Moscow 119421 Russia > Phone: +7(495)9362588 (office) > +7(916)5317022 (mobile) > Fax: +7(495)9361255 > e-mail: sasha]![photonics.ru > bagaturyants]![gmail.com >=20 >> From: owner-chemistry+sasha=3D=3Dphotonics.ru]![ccl.net > [mailto:owner-chemistry+sasha=3D=3Dphotonics.ru]![ccl.net] On Behalf Of Marce= l > Swart marcel.swart ~~ icrea.es > Sent: Monday, February 22, 2010 1:08 AM > To: Bagaturyants, Alexander A. > Subject: CCL: G03 Temperature Parameter >=20 >=20 > In any quantum-chemistry program, the temperature one can set on input ha= s > effect mainly > on the thermodynamic analysis, i.e. how the vibrational frequencies can b= e > transformed into > enthalpy, entropy and free energy. >=20 > The electronic energy, HOMO, LUMO, optimization, etc. are completely > independent of the > temperature.=A0 >=20 > Please read a good introductory textbook like Jensen's "Introduction to > computational=A0chemistry", > or any one of the introductory textbooks (Szabo/Ostlund, McWeeny, Leach, > Cramer, etc.). >=20 > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > dr. Marcel Swart >=20 > ICREA Research Professor at > Institut de Qu=EDmica Computacional > Universitat de Girona >=20 > Parc Cient=EDfic i Tecnol=F2gic > Edifici Jaume Casademont (despatx A-27) > Pic de Peguera 15 > 17003 Girona > Catalunya (Spain) >=20 > tel > +34-972-183240 > fax > +34-972-183241 > e-mail > marcel.swart*|*icrea.es > marcel.swart*|*udg.edu > web > http://www.marcelswart.eu > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script =3D->=20>=20>=20>=20>=20>=20>=20>=20>=20 >=20 From owner-chemistry@ccl.net Mon Feb 22 04:42:01 2010 From: ")yahoo.com" To: CCL Subject: CCL:G: G03 Temperature Parameter Message-Id: <-41312-100222043556-21731-yMrb+8NexAltLQVtnXpigA^^^server.ccl.net> X-Original-From: ahoo.com> Content-Type: multipart/alternative; boundary="0-338439507-1266831342=:64797" Date: Mon, 22 Feb 2010 01:35:42 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: ahoo.com] --0-338439507-1266831342=:64797 Content-Type: text/plain; charset=us-ascii Hereby I correct the mistake. I am doing a multi-step job.I needed the temperature for for analysis of the vibrational, rotational and translational energies although the job consists some geometry optimization and HOMO investigations in the primary step. Regards, A.F --- On Sun, 2/21/10, yahoo.com wrote: > From: yahoo.com Subject: CCL:G: G03 Temperature Parameter To: "yahoo.com> Date: Sunday, February 21, 2010, 6:21 AM Dear All, I would like to know how I can enter the environment temperature in my computations (i.e. Optimization, Energy, HOMO, etc. ) in Gaussian or any other software you recommend. Thank you in advance. Best regards, A.F --0-338439507-1266831342=:64797 Content-Type: text/html; charset=us-ascii


Hereby I correct the mistake. I am doing a multi-step job.I needed the temperature for for analysis of the vibrational, rotational and translational energies although the job consists some geometry optimization and HOMO investigations in the primary step.

Regards,
A.F


--- On Sun, 2/21/10, yahoo.com <owner-chemistry*ccl.net> wrote:

From: yahoo.com <owner-chemistry*ccl.net>
Subject: CCL:G: G03 Temperature Parameter
To: "*yahoo.com>
Date: Sunday, February 21, 2010, 6:21 AM

Dear All,
I would like to know how I can enter the environment temperature in my computations (i.e. Optimization, Energy, HOMO, etc. ) in Gaussian or any other software you recommend.

Thank you in advance.
Best regards,
A.F


--0-338439507-1266831342=:64797-- From owner-chemistry@ccl.net Mon Feb 22 06:41:00 2010 From: "Alex Naden anaden*_*fsmail.net" To: CCL Subject: CCL: Estimation of viscosity from molecular weight Message-Id: <-41313-100222063850-22259-GKHktYWhdU2/66/WTL6srg=-=server.ccl.net> X-Original-From: "Alex Naden" Date: Mon, 22 Feb 2010 06:38:46 -0500 Sent to CCL by: "Alex Naden" [anaden!=!fsmail.net] Hi Andreas, Thank you for your message and advice. I did not know about this program before so it is very helpful. Thank you. Best wishes, Alex From owner-chemistry@ccl.net Mon Feb 22 09:01:00 2010 From: "Ashwini B ashwinibilly[*]hotmail.com" To: CCL Subject: CCL: G03 Temperature Parameter Message-Id: <-41314-100222062914-21566-vTcxVJlN6W//A84TbFkzeA,server.ccl.net> X-Original-From: Ashwini B Content-Type: multipart/alternative; boundary="_43883da2-4acb-4652-ac55-87cd187bdb2e_" Date: Mon, 22 Feb 2010 10:59:59 +0000 MIME-Version: 1.0 Sent to CCL by: Ashwini B [ashwinibilly::hotmail.com] --_43883da2-4acb-4652-ac55-87cd187bdb2e_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear Sir=20 This is one simple example you can use to vary temperature. This is one sim= ple example for a multi-step job you can use to vary temperature mainly for= the analysis of the electronic=2C vibrational=2C rotational and translatio= nal energies. %chk=3DCH2.chk #p B3LYP/3-21G freq=3Dreadisotopes=20 CH2 0 1 C H 1 B1 H 1 B2 2 A1 B1 1.60097830 B2 1.60097830 A1 90.73220657 220.0 1.0 12 1 1 --Link1-- %chk=3DCH2.chk #p B3LYP/3-21G freq=3Dreadisotopes=20 CH2 0 1 C H 1 B1 H 1 B2 2 A1 B1 1.60097830 B2 1.60097830 A1 90.73220657 250.0 1.0 12 1 1 --Link1-- . . . . . . . . Hereby I correct the mistake. I am doing a multi-step job.I needed the temp= erature for for analysis of the vibrational=2C rotational and translational= energies although the job consists some geometry optimization and HOMO inv= estigations in the primary step. Regards=2C A.F =20 =20 _________________________________________________________________ Hotmail: Trusted email with Microsoft=92s powerful SPAM protection. https://signup.live.com/signup.aspx?id=3D60969= --_43883da2-4acb-4652-ac55-87cd187bdb2e_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Dear Sir
This is one simpl= e example you can use to vary temperature. This is one simple example for a multi-step job you can= use to vary temperature mainly for the analysis of the electronic=2C vibrational=2C rotational an= d translational energies.



%chk=3DCH2.chk
#p B3LYP/= 3-21G freq=3Dreadisotopes

CH2

0 1
 =3BC
 =3BH = =3B =3B =3B =3B =3B =3B =3B =3B =3B =3B=  =3B =3B =3B =3B =3B =3B =3B 1 =3B =3B&= nbsp=3B =3B =3B =3B =3B =3B =3B =3B =3B&nbs= p=3B =3B B1
 =3BH =3B =3B&n= bsp=3B =3B =3B =3B =3B =3B =3B =3B =3B = =3B =3B =3B =3B =3B =3B 1 =3B =3B =3B = =3B =3B =3B =3B =3B =3B =3B =3B =3B =3B= B2 =3B =3B =3B 2 =3B =3B =3B =3B =3B = =3B =3B =3B =3B =3B =3B =3B =3B A1

 =3B =3B B1 =3B =3B =3B =3B =3B =3B = =3B =3B =3B =3B =3B =3B 1.60097830
 =3B =3B B2 =3B =3B =3B =3B =3B&nbs= p=3B =3B =3B =3B =3B =3B =3B 1.60097830
 =3B =3B A1 =3B =3B =3B =3B&nb= sp=3B =3B =3B =3B =3B =3B =3B 90.73220657

220.0 1.0
12
1
1
=
--Link1--
%chk=3DCH2.chk
#p = B3LYP/3-21G freq=3Dreadisotopes

CH2
0 1
 =3BC
 =3BH =3B=  =3B =3B =3B =3B =3B =3B =3B =3B =3B&nb= sp=3B =3B =3B =3B =3B =3B =3B 1 =3B =3B&nbs= p=3B =3B =3B =3B =3B =3B =3B =3B =3B = =3B =3B B1
 =3BH =3B =3B&nb= sp=3B =3B =3B =3B =3B =3B =3B =3B =3B = =3B =3B =3B =3B =3B =3B 1 =3B =3B =3B = =3B =3B =3B =3B =3B =3B =3B =3B =3B =3B= B2 =3B =3B =3B 2 =3B =3B =3B =3B =3B = =3B =3B =3B =3B =3B =3B =3B =3B A1

 =3B =3B B1 =3B =3B =3B =3B =3B =3B = =3B =3B =3B =3B =3B =3B 1.60097830
 =3B =3B B2 =3B =3B =3B =3B =3B&nbs= p=3B =3B =3B =3B =3B =3B =3B 1.60097830
 =3B =3B A1 =3B =3B =3B =3B&nb= sp=3B =3B =3B =3B =3B =3B =3B 90.73220657

250.0 1.0
12
1
1
=
--Link1--

.
.
.
= .
.
.
.
.




Hereby I correct= the mistake. I am doing a multi-step job.I needed the temperature for for = analysis of the vibrational=2C rotational and translational energies althou= gh the job consists some geometry optimization and HOMO investigations in t= he primary step.

Regards=2C
A.F






Hotmail: Trusted email with Microsoft=92s powerful SPAM protection. Sig= n up now. = --_43883da2-4acb-4652-ac55-87cd187bdb2e_-- From owner-chemistry@ccl.net Mon Feb 22 12:59:00 2010 From: "Kaliappan Muthukumar muthukumar2k3_+_gmail.com" To: CCL Subject: CCL: POSCAR - Free Software Message-Id: <-41315-100222125711-11868-6sXkud2z1eAQSu4OJYRHSQ%a%server.ccl.net> X-Original-From: Kaliappan Muthukumar Content-Type: multipart/alternative; boundary=000325554592a5cc920480333c78 Date: Mon, 22 Feb 2010 11:50:55 -0500 MIME-Version: 1.0 Sent to CCL by: Kaliappan Muthukumar [muthukumar2k3.:.gmail.com] --000325554592a5cc920480333c78 Content-Type: text/plain; charset=ISO-8859-1 Dear Folks, I am trying to create a VASP POSCAR files with more than 100's atom in my structure. I wish few of these atoms to be frozen and i am able to do that manually. Since, editing becomes cumbersome for more than 100's of atoms, (If i need to work on multiple files) i request any of you to let me know, if you are aware of any '*free*' software that could help me to make VASP Poscar files (with the option to freeze some of the atoms in it). I have information about goVasp and MedeA, but they are not free. Look forward hearing from you. Many thanks in advance. Best regards, Muthu -- Dr. Muthukumar Kaliappan, Post-doctoral Research Assistant Dept. of Chem. and Mater. Engg. University of Cincinnati, Cincinnati, Ohio, USA Phone : 513 787 2720 Email : Kaliappan.Muthukumar#gmail.com --000325554592a5cc920480333c78 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Folks,

I am trying to create a VASP POSC= AR files with more than
100's atom in my structure.

I wish few of these atoms to be frozen and i am able to do = that
manually.=A0

Since, editing becomes cumbersom= e for more than 100's of
atoms, (If i need to work on multipl= e files) i request any of you to let me know, if you are aware of
any 'free'=A0software=A0that could help me to make VA= SP Poscar files (with the option
to freeze some of the atoms in i= t).

I have information about goVasp and MedeA, but= they are not free.=A0

Look forward hearing from you.=A0

<= div>Many thanks in advance.

Best regards,
Muthu









=





--
Dr. = Muthukumar Kaliappan,
Post-doctoral Research Assistant
Dept. of Chem= . and Mater. Engg.
University of Cincinnati,
Cincinnati,
Ohio, USA

Phone : 513 7= 87 2720
Email =A0: Kal= iappan.Muthukumar#gmail.com
--000325554592a5cc920480333c78-- From owner-chemistry@ccl.net Mon Feb 22 14:41:01 2010 From: "Babak Khalili khalili.babak++gmail.com" To: CCL Subject: CCL: POSCAR - Free Software Message-Id: <-41316-100222143707-16295-jUeM7HpEtDb3J95ldP4UaQ#,#server.ccl.net> X-Original-From: Babak Khalili Content-Type: text/plain; charset=UTF-8 Date: Mon, 22 Feb 2010 11:36:53 -0800 MIME-Version: 1.0 Sent to CCL by: Babak Khalili [khalili.babak/./gmail.com] Dear Muthu, May you please give me the web address, where I can download it? Have a nice time, Babak On 2/22/10, Kaliappan Muthukumar muthukumar2k3_+_gmail.com wrote: > Dear Folks, > > I am trying to create a VASP POSCAR files with more than > 100's atom in my structure. > > I wish few of these atoms to be frozen and i am able to do that > manually. > > Since, editing becomes cumbersome for more than 100's of > atoms, (If i need to work on multiple files) i request any of you to let me > know, if you are aware of > any '*free*' software that could help me to make VASP Poscar files (with the > option > to freeze some of the atoms in it). > > I have information about goVasp and MedeA, but they are not free. > > Look forward hearing from you. > > Many thanks in advance. > > Best regards, > Muthu > > > > > > > > > > > > > > > -- > Dr. Muthukumar Kaliappan, > Post-doctoral Research Assistant > Dept. of Chem. and Mater. Engg. > University of Cincinnati, > Cincinnati, > Ohio, USA > > Phone : 513 787 2720 > Email : Kaliappan.Muthukumar^_^gmail.com > -- http://www.iccst2010.fa.itb.ac.id/ From owner-chemistry@ccl.net Mon Feb 22 15:15:00 2010 From: "Vincent Leroux vincent.leroux[*]loria.fr" To: CCL Subject: CCL: AW: can you recommend software to compare chemical databases and exclude duplicates pls Message-Id: <-41317-100222131600-19206-9zUnCXGfQDLavvFBqBypyA%server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 22 Feb 2010 19:15:44 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux*loria.fr] Hi Wolf, It is clear that the approach I am proposing is just a gross outline, and there might be some more suited variants. The first of those might be to go for ScreeningAssistant. Other possibilities, simply adding the InChI key to the MDL tags (or the name field, in addition to the supplier's name) then do tag-based processing, or use canonicalized SMILES instead of InChI. But for the moment, would you please share your personal experience by documenting your criticisms precisely. Reproductible examples would be very constructive as they might: - prove I was, with some colleagues, incredibly lucky in our past use of some such "non viable" approaches, - help the InChI and OpenBabel developers improve their code, - warn users of the possible pitfalls with these tools. In particular, I would be greatly interested in clear cases of issues with InChI decoding its own strings, (Open)Babel failing despite input data complying to the file format specifications, and "blank coordinates" SDF files causing "problems" compared to "2D representations". Thanks in advance VL Le 21/02/10 12:59, Wolf-D. Ihlenfeldt wdi/./xemistry.com a écrit : > > Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi[#]xemistry.com] > > Ahem - IMHO the outline below is really *NOT* a viable solution. > > Relying on the ability to decode InChI strings back into a graph is an > unsuitable approach. InChI was not designed for this. The current > implementations of inverters fail on a significant number of strings, and on > others the results are often pretty weird tautomers if you have mobile H. > > Also, last I checked OpenBabel did not generate 2D representations - an > regenerated SD file will have all-0 atomic coordinates, which can be a > problem later. And OpenBabel has in general a lot of problems with > stereochemistry - if you need stereochemistry in your project, my personal > advice is to stay away from it. > > > software to compare chemical databases >> and exclude duplicates pls >> >> >> Sent to CCL by: Vincent Leroux [vincent.leroux+*+loria.fr] >> >> Hi Andrew, >> >> There is ScreeningAssistant for such a task, and much more. >> http://hal.archives- >> ouvertes.fr/docs/00/07/97/12/PDF/monge_Molecular_Diversity_revised_2.pd >> f >> http://dx.doi.org/10.1007/s11030-006-9033-5 >> http://dx.doi.org/10.2174/157340908785747410 >> >> SA is really boxing in the heavyweight category of chemoinformatics >> tools so you might prefer to process data by yourself. >> My suggestions : >> >> - first "clean up" db1.sdf and db2.sdf: remove salts, hydrogens etc. >> everything in the structure that might differ artificially from one >> supplier to the other. (Open)Babel should do a good job here. >> >> - name all molecules in db1.sdf and db2.sdf using scripts. The name >> must >> be on the 1st line in each molecule record and should not contain >> spaces. You want a combination of the supplier name and the molecule >> supplier's unique ID (already in place if you are lucky, else found in >> some MDL tag). Make sure the name does not contain spaces, and that is >> is put in the correct position (1st line). >> >> - use the InChI software for generating db1.inchi and db2.inchi, and >> make sure you get text files with 1 line per molecule formatted like: >> >> >> - If the molecules are named Supplier1/ and >> Supplier2/ , then use the following commands (have not >> tested them, but should work) >> >> cat db[12].inchi | sort -k2 | uniq -s 1 - | grep '^Supplier1/' > >> db1_unique.inchi >> cat db[12].inchi | sort -k2 | uniq -s 1 - | grep '^Supplier2/' > >> db2_unique.inchi >> cat db[12].inchi | sort -k2 | uniq -d -s 1 - | awk '{l=$1; getline; >> print l"_aka_"$0}' > db12_common.inchi >> >> This will generate db1_unique.inchi, db2_unique.inchi and >> db12_common.inchi - self-explanatory. >> >> - use OpenBabel (or equivalent software) for converting your InChI >> files >> to SDF format/2D representation, then Corina (or equivalent) if you >> want >> 3D coordinates, e.g. for docking. >> >> Regards, >> VL >> >> >> >> Le 19/02/10 18:45, Andrew Voronkov drugdesign:yandex.ru a écrit : >>> >>> Sent to CCL by: Andrew Voronkov [drugdesign%yandex.ru] >>> Dear CCL users, >>> can you please recommend me academics free software or scripts (or >> software with good evaluation period) for comparison of databases. For >> example I want to download two publically available databases and unite >> them excluding duplicates into a separate database. So in this case I >> ll get one united database and one database where duplicate compounds >> will be (but not duplicated). Can you please suggest such software? >>> >>> Sincerely yours, >>> Andrew >>> >>> >> > > > > -=his is automatically added to each message by the mailing script =-> > > From owner-chemistry@ccl.net Mon Feb 22 15:51:01 2010 From: "Christopher Cramer cramer:_:umn.edu" To: CCL Subject: CCL: Farewell to Bjorn Roos Message-Id: <-41318-100222144122-16792-WaVp+qXFl8iENqxW61+LEw],[server.ccl.net> X-Original-From: "Christopher Cramer" Date: Mon, 22 Feb 2010 14:41:18 -0500 Sent to CCL by: "Christopher Cramer" [cramer%%umn.edu] Today brings the sad news that Professor Bjorn Roos of Lund University has passed away. I subscribe to the belief that practitioners of science should appreciate not only the technical aspects of their field, but also the human history that underlies its development. In that vein, I hope that CCL readers will find the below summary of Bjorn's scientific accomplishments to be of interest. His insights, and his delicious irascibility, which was always tempered with humor, will be sorely missed by his many friends and colleagues, and the broader scientific community in general. I note that his name, Bjorn, should carry a diacritical umlaut on the "o", but I have left it off to ensure email portability, and somehow "Bjoern" simply doesn't seem quite right... In any case: Professor Roos' contributions to theoretical chemistry were foundational at the most fundamental level: each of his developments opened some broad new area of chemistry that had hitherto seen little successful theoretical study. Professor Roos' models continue to be put to practical use every day in modern calculations, and in many cases continue to be the benchmark calculations against which new model developments are measured. Professor Roos began his studies of quantum chemistry just as the community was beginning to recognize the potential for digital computers to assist in the solution of the complex numerical problems associated with solution of the Schrdinger equation for molecular systems. His first major breakthrough was the development of the direct configuration interaction (CI) method in 1972. In a particularly clever insight, Professor Roos recognized that the very expensive formation and diagonalization of the CI matrix could be replaced by an iterative procedure involving only the two-electron repulsion integrals already available from an antecedent Hartree-Fock (HF) calculation. This algorithmic advance reduced the time required for a typical CI calculation by one to two orders of magnitude for a typical molecular system. Early applications of this paradigm- shifting approach included the determination of the bond energy in the water dimer with an accuracy of better than 1 kcal/mol, the identification of hydrogen isocyanide (HNC) in interstellar space through comparison to its computed rotational spectrum, and the calculation of the energy surface for H3 with an accuracy of 0.1 kcal/mol (the latter work involved Roos' then student, Per Siegbahn, now Professor at Stockholm University). Professor Roos' next key development came in 1980, when he and his co-workers described the complete active space self-consistent field (CASSCF) method. Prior to this point, theoretical studies had focused predominantly on closed-shell singlets and other electronic states readily described by single determinants. The CASSCF model, however, was completely general and opened the way to even-handed treatment of all types of electronic structures, independent of open shell character, spin multiplicity, etc. Thus, using the CASSCF model, it became possible to generate accurate potential energy surfaces across regions of bond making and bond breaking (i.e., to study chemical reactions) and also to rigorously describe excited molecular electronic states. The CASSCF method continues to be one of the most important standard tools in quantum chemistry for the calculation of complex molecular properties in both ground and excited states of molecular systems. Indeed, it is still the only method which can be used for the general treatment of excited-state potential energy surfaces (photochemistry) although newly developed models based on time-dependent density functional theory are beginning to show promise. Professor Roos has recently extended the CASSCF model to permit spin-orbit coupling between different electronic states. The combination of this model with a Douglas-Kroll-Hess Hamiltonian (to account for scalar relativistic effects) has led to an explosion of activity in the application of the CASSCF model to lanthanide and actinide compounds, including a fascinating paper in Nature in 2005 that addressed the unique bonding in the U2 dimer and led to a renaissance of interest in the fundamental nature of the chemical bond. In typical application, the CASSCF method treats only the so-called nondynamical part of the electron-electron correlation problem. The missing part (dynamical correlation) can be treated using a multireference (MR) variation of Roos' direct CI, but such a direct MRCI can only be practically undertaken for very small molecules. Recognizing this limitation, Roos contributed yet another fundamental methodological advance and developed over the course of the 1980s a multireference perturbation theory for computing the electron correlation energy: CASPT2. The CASSCF/CASPT2 model has proven to be remarkably accurate and robust, making it the model of choice for the study of many reactions and, particularly, for the study of photochemistry and excited-state reactivity. In the absence of an experimental measurement, the typical benchmark for an excited-state energy would be a CASPT2 calculation. One measure of the utility and popularity of the CASSCF/CASPT2 model is the degree to which it has been coded into the most widely used electronic structure program suites, including the one developed by Professor Roos himself, MOLCAS, which has a user base of hundreds of research groups. Professor Roos' approach to quantum chemistry was always to develop methods which could be used in large-scale applications to real chemical problems. He and his co-workers demonstrated the scope of his methodologies in pioneering applications, e.g., characterizing the spectroscopic properties of the blue copper proteins (which led to a new understanding of the concept of strain in biochemistry), describing the electronic spectra of numerous organic molecules, including the DNA and amino acid chromophores, and studying the chemical bonds in transition-metal compounds (to include the only successful description to date of the chemical bond in Cr2). As noted above, particularly recent applications have focused on the heaviest elements in the periodic table, including studies of the dynamics of the uranyl ion in water, and the characterization of complexes of uranyl and neptunyl with carbonate and water (relevant to the reprocessing of spent nuclear fuel). Key to several of these studies ws also Roos' development of especially well balanced basis sets for all-electron calculations, and recent and important developments using Cholesky decomposition to speed integral evaluation, (the latter area involving Roos' long-time co-worker Roland Lindh, Lecturer at Lund and now Professor at Uppsala). The methodological developments pioneered by Professor Roos dramatically and uniquely advanced wave-function theories in quantum chemistry. The influence of the direct CI, CASSCF, and CASPT2 models on modern quantum chemistry have been profound, particularly in the degree to which they have permitted the extension of accurate theoretical models to enormous swaths of the periodic table that had been previously inaccessible. This is a testament to the creativity and vision of Professor Roos, who repeatedly combined an appreciation for chemical relevance with brilliant physical and algorithmic insights. In San Francisco, at the upcoming spring National Meeting of the American Chemical Society, Bjorn was to have received the ACS Award in Theoretical Chemistry. Roland Lindh and Laura Gagliardi will be presenting on his behalf during the award symposium in the Division of Physical Chemistry. I have no doubt that attendees who knew him better than I will be able to share more stories of Bjorn, including especially those that go beyond his prodigious scientific accomplishments, and I look forward to the chance to learn more about him there. Respectfully, Chris Cramer University of Minnesota From owner-chemistry@ccl.net Mon Feb 22 16:28:00 2010 From: "Greg Warren greg,eyesopen.com" To: CCL Subject: CCL: Redocking with Fred docking tool Message-Id: <-41319-100222145451-22571-lph1d/9M5cpjiJA+e9QFsw/a\server.ccl.net> X-Original-From: Greg Warren Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 22 Feb 2010 11:24:19 -0800 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg_+_eyesopen.com] Dear Vinod, Please check the user manual for FRED, specifically chapter 6 pages 43-70. = There are a number of examples of command lines starting from the simple t= o the complex on how to use FRED for redocking. Regards, Greg -----Original Message----- > From: owner-chemistry+greg=3D=3Deyesopen.com^^^ccl.net [mailto:owner-chemistr= y+greg=3D=3Deyesopen.com^^^ccl.net] On Behalf Of Vinod kasam vinod.kasam_-_uk= y.edu Sent: Wednesday, February 17, 2010 11:59 AM To: Greg Warren Subject: CCL: Redocking with Fred docking tool Sent to CCL by: "Vinod kasam" [vinod.kasam^^uky.edu] Dear all I am a new user of Fred docking tool.=20 Can somebody please tell me the syntax to perform redocking with Fred. I wa= nt to see the RMSD against a set of PDBs. I using Fred 2.2.5 version. Thanks in advance, -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt