From owner-chemistry@ccl.net Wed Jun 15 07:48:01 2011 From: "Sergio Manzetti sergio.manzetti__gmail.com" To: CCL Subject: CCL:G: Estimate binding energy between three molecules Message-Id: <-44897-110615074239-23338-XS9ZZdKgX045BGT2mR9KbA~!~server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Wed, 15 Jun 2011 07:42:37 -0400 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti=gmail.com] Dear CCL users. I have batched through three B3LYP-6-311G (d,**) Gaussian 03 calculations with three molecules, A, B, and C, adjacent to each other in the order: Calculation 1: A Calculation 2: A-B Calculation 3: C-A-B I would like to estimate the binding energy between A-B in calculation 2 and 3. How do I do this with the output Gaussian log file? I have a program called GabEdit, but am not sure how to get kj/mol with any of these programs and results. Thank you best wishes From owner-chemistry@ccl.net Wed Jun 15 11:29:00 2011 From: "Diogo Volpati volpati(_)fct.unesp.br" To: CCL Subject: CCL: Gaussian Doubts - Eosin Optimization Message-Id: <-44898-110614215621-15615-fCXFnLaGUOcxVY3OwlqzjQ%a%server.ccl.net> X-Original-From: "Diogo Volpati" Date: Tue, 14 Jun 2011 21:56:20 -0400 Sent to CCL by: "Diogo Volpati" [volpati|-|fct.unesp.br] Dear All, I am trying to optimize the eosin molecule. As a first approach, I used the following basis set configuration: %chk=C:/Users/Usuario/Desktop/Calculos Tericos/eosin.chk %mem=6MW %nproc=1 ----------------------------------------------- #p opt=tight b3lyp/6-31g(d,p) geom=connectivity After 11 days 3 hours 18 minutes 22.0 seconds, the job finished via link 9999. The job consumed the 210 cycles trying to optimize the energy without success!!! Bad I could see that energy is oscillating after cycle number 16. I consulted some jobs that have used keywords like maxcycle=N and IOP(1/8=n) to solve the problem. But, I could not to do it! My doubt are: 1 - What is command necessary to restart the calculation from the checkpoint file? I tried the command below with no success: #p opt=(restart,calcfc,tight,notrustupdate) b3lyp/6-31g(d,p) iop(1/8=10) 2- Do I need to put all the commands again and still read the checkpoint file to restart the optimization? 3- Are there some magic value N for keywords maxcycle=N and Iop(1/8=N) work well? I apologize if my doubts are simple and trivial. I just started in this new world of computational chemistry. I really appreciate any help . Thanks a lot in advance and best regards Ms. Diogo Volpati Physics, Chemistry and Biology Department Technology and Science Faculty So Paulo State University UNESP Brazil From owner-chemistry@ccl.net Wed Jun 15 12:04:00 2011 From: "Diogo Volpati divolpati#yahoo.com.br" To: CCL Subject: CCL: Gaussian Problems - Checkpoint file Message-Id: <-44899-110615113321-9603-XbMpU7owIELDtdQTjohdrw|*|server.ccl.net> X-Original-From: "Diogo Volpati" Date: Wed, 15 Jun 2011 11:33:19 -0400 Sent to CCL by: "Diogo Volpati" [divolpati]^[yahoo.com.br] Dear All, I am trying to optimize the eosin molecule. As a first approach, I used the following basis set configuration: %chk=C:/Users/Usuario/Desktop/Calculos Tericos/eosin.chk %mem=6MW %nproc=1 ----------------------------------------------- #p opt=tight b3lyp/6-31g(d,p) geom=connectivity After 11 days 3 hours 18 minutes 22.0 seconds, the job finished via link 9999. The job consumed the 210 cycles trying to optimize the energy without success!!! Bad I could see that energy is oscillating after cycle number 16. I consulted some jobs that have used keywords like maxcycle=N and IOP(1/8=n) to solve the problem. But, I could not to do it! My doubt are: 1 - What is command necessary to restart the calculation from the checkpoint file? I tried the command below with no success: #p opt=(restart,calcfc,tight,notrustupdate) b3lyp/6-31g(d,p) iop(1/8=10) 2- Do I need to put all the commands again and still read the checkpoint file to restart the optimization? 3- Are there some magic value N for keywords maxcycle=N and Iop(1/8=N) work well? I apologize if my doubts are simple and trivial. I just started in this new world of computational chemistry. I really appreciate any help . Thanks a lot in advance and best regards Ms. Diogo Volpati Physics, Chemistry and Biology Department Technology and Science Faculty So Paulo State University UNESP Brazil From owner-chemistry@ccl.net Wed Jun 15 12:39:00 2011 From: "Ivanciuc, Ovidiu I. oiivanci:utmb.edu" To: CCL Subject: CCL: sources for chemical dscriptors Message-Id: <-44900-110615112219-10401-13oPfKaJfIeO/iTHOycaNQ]*[server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 15 Jun 2011 10:22:01 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci!^!utmb.edu] A comprehensive description of molecular descriptors used in QSAR and virtual screening may be found in: R.Todeschini and V.Consonni: "Molecular Descriptors for Chemoinformatics", (2 volumes), WILEY-VCH,Weinheim (Germany) 2009, 1257 pp More than 1600 molecular descriptors can be computed with E-DRAGON: http://www.vcclab.org/lab/edragon/ CODESSA also can compute a large number of molecular descriptors, more than 1000 if MOPAC calculations are included. Both DRAGON and CODESSA are highly used in QSAR, but for virtual screening it is more useful to compute fingerprints and pharmacophores. PaDEL-Descriptor is a recent package which can compute fingerprints: "The software currently calculates 801 descriptors (667 1D, 2D descriptors and 134 3D descriptors) and 10 types of fingerprints. The descriptors and fingerprints are calculated using The Chemistry Development Kit with some additional descriptors and fingerprints" (from PaDEL-Descriptor web page) For a review on pharmacophores, see the paper: Monty Kier and the Origin of the Pharmacophore Concept http://www.biochempress.com/av06_0271.html To learn about graph descriptors and topological indices see the reviews: http://ivanciuc.org/iorg_bchap.html O ________________________________________ > From: owner-chemistry+oiivanci==utmb.edu[a]ccl.net [owner-chemistry+oiivanci==utmb.edu[a]ccl.net] On Behalf Of sajeev r sajucheminformatics^^^gmail.com [owner-chemistry[a]ccl.net] Sent: Sunday, June 12, 2011 5:16 AM To: Ivanciuc, Ovidiu I. Subject: CCL: sources for chemical dscriptors Hello members, I am in search of new chemical descriptor, could anyone tell what are the different sources available ?.for eg. I have collected some descriptors from various sources like physical chemistry,organic chemistry, graph theory, quantum chemistry etc... regards -- Sajeev R Research Scholar Cheminformatics Centre. Malabar Christian College Calicut-673001 Kerala, India. phone :09846041423 email :sajucheminformatics+/-gmail.com From owner-chemistry@ccl.net Wed Jun 15 13:13:01 2011 From: "Nuno A. G. Bandeira nuno.bandeira]-[ist.utl.pt" To: CCL Subject: CCL:G: Gaussian Problems - Checkpoint file Message-Id: <-44901-110615125517-30492-WwyaGV/ahFohug0Mzf94xw{:}server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 15 Jun 2011 18:55:07 +0200 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira,,ist.utl.pt] Dear Diogo, Try to establish if your start geometry is good. With Gaussian if you exhaust your optimisation cycles you can't restart anew with Opt=restart. You'll have to re-use the geometry and wavefunction from the last cycle with Geom=AllCheck and Guess=Read as well as resetting MaxCycle. Best wishes, Nuno -- Nuno A. G. Bandeira, AMRSC Departamento de Qumica Fsica i Inorgnica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.l Domingo 43007 Tarragona - SPAIN -- From owner-chemistry@ccl.net Wed Jun 15 13:48:00 2011 From: "Tobias Kraemer tobias.kraemer===chem.ox.ac.uk" To: CCL Subject: CCL:G: ASyTop Error in Gaussian09 Message-Id: <-44902-110615132905-17831-yqr0XePmZNqT5wUlt9Nefw#,#server.ccl.net> X-Original-From: Tobias Kraemer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 15 Jun 2011 18:28:56 +0100 MIME-Version: 1.0 Sent to CCL by: Tobias Kraemer [tobias.kraemer#,#chem.ox.ac.uk] Dear CCLers.... I have a problem with Gaussian09, which produces a "Logic error in ASyTop", when I try to do a calculation on a bipyridine molecule. Does anyone know what this error means (must be related to symmetry). I have tried various dihedral angles between the two ring moieties, without success, and also included the nosymm option, equally, without much success. Here is my input, any comments are appreciated. %NProc=8 %Mem=8000MB %chk=bipy_neutral_planar #P opt um052X/tzvp scf=tight gfinput gfprint pop=full 4,4'-bipy neutral 0 1 6 -1.839122000 0.000000000 -2.438600000 6 -1.384016129 1.098723995 -3.159448000 6 -2.294228608 -1.098723319 -3.159448000 6 -1.405858792 1.047352926 -4.544367000 1 -1.040148263 1.988925608 -2.654093000 6 -2.272385946 -1.047352251 -4.544367000 1 -2.638096474 -1.988924932 -2.654093000 7 -1.839122000 0.000000000 -5.238321000 1 -1.063069966 1.893696689 -5.124296000 1 -2.615174771 -1.893696013 -5.124296000 6 -1.839122000 0.000000000 -0.960493000 6 -1.384016129 -1.098723995 -0.239645000 6 -2.294228608 1.098723319 -0.239645000 1 -2.638096474 1.988924932 -0.745000000 1 -1.040148263 -1.988925608 -0.745000000 6 -2.272385946 1.047352251 1.145274000 6 -1.405858792 -1.047352926 1.145274000 1 -2.615174771 1.893696013 1.725204000 1 -1.063069966 -1.893696689 1.725204000 7 -1.839122000 0.000000000 1.839228000 Thanks Tobi -- _________________________________________ dipl.-chem. tobias krmer department of chemistry inorganic chemistry laboratory university of oxford south parks road oxford OX1 3QR united kingdom |phone| +44 (0)1865 272 135 |email| tobias.kraemer|chem.ox.ac.uk |email| tobias.kraemer|linacre.ox.ac.uk _________________________________________ From owner-chemistry@ccl.net Wed Jun 15 14:42:00 2011 From: "nicho demus mnichodemus,,yahoo.com" To: CCL Subject: CCL: PDB Survey Message-Id: <-44903-110615123126-6575-H5IVQXy0+sYMytU0Ehv1WA]~[server.ccl.net> X-Original-From: nicho demus Content-Type: multipart/alternative; boundary="0-492306046-1308155477=:92349" Date: Wed, 15 Jun 2011 22:01:17 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: nicho demus [mnichodemus-,-yahoo.com] --0-492306046-1308155477=:92349 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable you are on the right place only.the work you are doing is called protein-li= gand docking.lot of softwares are available for this purpose,some of them a= re autodock,argus lab,discovery studio,schrodinger and so on. --- On Tue, 14/6/11, Eliac Brown Eliacbrown _ yahoo.com wrote: > From: Eliac Brown Eliacbrown _ yahoo.com Subject: CCL: PDB Survey To: "Maria Arockiam, Nichodemus " Date: Tuesday, 14 June, 2011, 9:09 AM Sent to CCL by: "Eliac=A0 Brown" [Eliacbrown_+_yahoo.com] Dear CCL First of all, I am sorry if it is not the right place to post of question. I am looking for a certain types of proteins interact with the ligand via n= on=20 covalent interaction. Is there any software/website can be used used for this job? The search should be base on the distance between the ligand atom type and = the=20 protein. I used isostar software, and looking for another one. Thanks in advance Eliac -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0--0-492306046-1308155477=:92349 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
you are on the right place only.the work you = are doing is called protein-ligand docking.lot of softwares are available f= or this purpose,some of them are autodock,argus lab,discovery studio,schrod= inger and so on.

--- On Tue, 14/6/11, Eliac Brown Eliacbrown _ ya= hoo.com <owner-chemistry[*]ccl.net> wrote:

From: Eliac Brown Eliacbrown _ yahoo.com <owne= r-chemistry[*]ccl.net>
Subject: CCL: PDB Survey
To: "Maria Arockiam,= Nichodemus " <mnichodemus[*]yahoo.com>
Date: Tuesday, 14 Ju= ne, 2011, 9:09 AM


Sent to CCL by: "Eliac  Brown" [Eliacbrown_= +_yahoo.com]
Dear CCL
First of all, I am sorry if it is not the right= place to post of question.
I am looking for a certain types of proteins= interact with the ligand via non
covalent interaction.
Is there any= software/website can be used used for this job?
The search should be ba= se on the distance between the ligand atom type and the
protein.
I u= sed isostar software, and looking for another one.
Thanks in advance
= Eliac



-=3D This is automatically added to each message by th= e mailing script =3D-
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--0-492306046-1308155477=:92349-- From owner-chemistry@ccl.net Wed Jun 15 15:56:00 2011 From: "eurisco1^^^pochta.ru" To: CCL Subject: CCL:G: ASyTop Error in Gaussian09 Message-Id: <-44904-110615155417-4609-qJrEoFBxocpog82paPG/BQ=-=server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="UTF-8"; reply-type=response Date: Wed, 15 Jun 2011 23:55:34 +0400 MIME-Version: 1.0 Sent to CCL by: [eurisco1__pochta.ru] Dear Tobias Kraemer, Maybe opt(Cartesian) is the solution for this case. Sincerely, Ol Ga -----Исходное сообщение----- > From: Tobias Kraemer tobias.kraemer===chem.ox.ac.uk Sent: Wednesday, June 15, 2011 9:28 PM To: Ga, Ol Subject: CCL:G: ASyTop Error in Gaussian09 Sent to CCL by: Tobias Kraemer [tobias.kraemer#,#chem.ox.ac.uk] Dear CCLers.... I have a problem with Gaussian09, which produces a "Logic error in ASyTop", when I try to do a calculation on a bipyridine molecule. Does anyone know what this error means (must be related to symmetry). I have tried various dihedral angles between the two ring moieties, without success, and also included the nosymm option, equally, without much success. Here is my input, any comments are appreciated. %NProc=8 %Mem=8000MB %chk=bipy_neutral_planar #P opt um052X/tzvp scf=tight gfinput gfprint pop=full 4,4'-bipy neutral 0 1 6 -1.839122000 0.000000000 -2.438600000 6 -1.384016129 1.098723995 -3.159448000 6 -2.294228608 -1.098723319 -3.159448000 6 -1.405858792 1.047352926 -4.544367000 1 -1.040148263 1.988925608 -2.654093000 6 -2.272385946 -1.047352251 -4.544367000 1 -2.638096474 -1.988924932 -2.654093000 7 -1.839122000 0.000000000 -5.238321000 1 -1.063069966 1.893696689 -5.124296000 1 -2.615174771 -1.893696013 -5.124296000 6 -1.839122000 0.000000000 -0.960493000 6 -1.384016129 -1.098723995 -0.239645000 6 -2.294228608 1.098723319 -0.239645000 1 -2.638096474 1.988924932 -0.745000000 1 -1.040148263 -1.988925608 -0.745000000 6 -2.272385946 1.047352251 1.145274000 6 -1.405858792 -1.047352926 1.145274000 1 -2.615174771 1.893696013 1.725204000 1 -1.063069966 -1.893696689 1.725204000 7 -1.839122000 0.000000000 1.839228000 Thanks Tobi -- _________________________________________ dipl.-chem. tobias krämer department of chemistry inorganic chemistry laboratory university of oxford south parks road oxford OX1 3QR united kingdom |phone| +44 (0)1865 272 135 |email| tobias.kraemer{=}chem.ox.ac.uk |email| tobias.kraemer{=}linacre.ox.ac.uk _________________________________________http://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 Jun 15 16:46:01 2011 From: "Serghei Glinca glinca{=}staff.uni-marburg.de" To: CCL Subject: CCL: PDB Survey Message-Id: <-44905-110615135646-21348-QluyFHLPkH394n21KjIFWQ=-=server.ccl.net> X-Original-From: Serghei Glinca Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 15 Jun 2011 19:56:13 +0200 MIME-Version: 1.0 Sent to CCL by: Serghei Glinca [glinca!A!staff.uni-marburg.de] Hello Eliac! You could try Relibase+. Basically, it was designed to mine protein-ligand interactions. For example, using the Relibase Sketcher you can define what kind of interactions you are looking for, via a GUI. Using reliscript (Python interface to the database) you can also create more complex queries. You have already used Isostar. CCDC also provides Relibase. Cheers, Serghei On 14.06.2011 16:09, Eliac Brown Eliacbrown _ yahoo.com wrote: > Sent to CCL by: "Eliac Brown" [Eliacbrown_+_yahoo.com] > Dear CCL > First of all, I am sorry if it is not the right place to post of question. > I am looking for a certain types of proteins interact with the ligand via non > covalent interaction. > Is there any software/website can be used used for this job? > The search should be base on the distance between the ligand atom type and the > protein. > I used isostar software, and looking for another one. > Thanks in advance > Eliac> > -- Serghei Glinca Group of Prof. Dr. G. Klebe Department of Pharmaceutical Chemistry University of Marburg Marbacher Weg 6 D-35032 Marburg, Germany Phone: +49 6421 28-25930 Email: glinca^staff.uni-marburg.de Homepage: www.agklebe.de From owner-chemistry@ccl.net Wed Jun 15 20:07:00 2011 From: "quartarolo::unical.it" To: CCL Subject: CCL: Gaussian Doubts - Eosin Optimization Message-Id: <-44906-110615172704-3235-gaNt/bIrLhW/QgQiSOzzeQ###server.ccl.net> X-Original-From: quartarolo%%unical.it Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 15 Jun 2011 23:26:50 +0200 MIME-Version: 1.0 Sent to CCL by: quartarolo a unical.it Hello, Your molecule seems very simple to optimize. Sometimes a bad starting geometry or other not-well defined input parameters, such as charge and multiplicity, in my modest experience, can complicate your job. If you can attach your input and output files, may be someone can give more insights to your problem. best regards Quartarolo Domenico University of Calabria, Rende (Italy) Def. Quota "Diogo Volpati volpati(_)fct.unesp.br" : > > Sent to CCL by: "Diogo Volpati" [volpati|-|fct.unesp.br] > Dear All, > I am trying to optimize the eosin molecule. As a first approach, I used the > following basis set configuration: > > %chk=C:/Users/Usuario/Desktop/Calculos Tericos/eosin.chk > %mem=6MW > %nproc=1 > ----------------------------------------------- > #p opt=tight b3lyp/6-31g(d,p) geom=connectivity > > After 11 days 3 hours 18 minutes 22.0 seconds, the job finished via link > 9999. The job consumed the 210 cycles trying to optimize the energy without > success!!! Bad > I could see that energy is oscillating after cycle number 16. I consulted > some jobs that have used keywords like maxcycle=N and IOP(1/8=n) to solve the > problem. But, I could not to do it! My doubt are: > > 1 - What is command necessary to restart the calculation from the checkpoint > file? I tried the command below with no success: > #p opt=(restart,calcfc,tight,notrustupdate) b3lyp/6-31g(d,p) iop(1/8=10) > > 2- Do I need to put all the commands again and still read the checkpoint file > to restart the optimization? > > 3- Are there some magic value N for keywords maxcycle=N and Iop(1/8=N) work > well? > > I apologize if my doubts are simple and trivial. I just started in this new > world of computational chemistry. > I really appreciate any help . Thanks a lot in advance and best regards > > Ms. Diogo Volpati > Physics, Chemistry and Biology Department > Technology and Science Faculty > So Paulo State University UNESP > Brazil> > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. **** Riservatezza / Confidentiality **** In ottemperanza al D.Lgs. n. 196 del 30/6/2003 in materia di protezione dei dati personali, le informazioni contenute in questo messaggio sono strettamente riservate ed esclusivamente indirizzate al destinatario indicato (oppure alla persona responsabile di rimetterlo al destinatario). Vogliate tener presente che qualsiasi uso, riproduzione o divulgazione di questo messaggio e' vietato. Nel caso in cui aveste ricevuto questo messaggio per errore, vogliate cortesemente avvertire il mittente e distruggere il presente messaggio.