From owner-chemistry@ccl.net Tue Mar 16 00:03:00 2010 From: "rocky walden rocky.walden19],[gmail.com" To: CCL Subject: CCL: Water molecules participating in Enzymatic Reactions Message-Id: <-41444-100315232958-17075-jrCl9C53LzcYN7C5MMvWgg[-]server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=0016e6498a5cf6d9bc0481e29b18 Date: Tue, 16 Mar 2010 08:59:45 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19*gmail.com] --0016e6498a5cf6d9bc0481e29b18 Content-Type: text/plain; charset=ISO-8859-1 Hiii For this you can try this application Water Map from Schrodinger Here is the doi of an article using Water Map 10.1002/pro.177 (wiley interscience) Title: High-energy water sites determine peptide binding affinity and specificity of PDZ domains. Thanks Rocky On Mon, Mar 15, 2010 at 10:50 PM, Lochana C Menikarachchi lochanac^^ yahoo.com wrote: > > Sent to CCL by: "Lochana C Menikarachchi" [lochanac#,#yahoo.com] > Dear All, > > I need to model an enzymatic reaction in which explicit water molecules > participate in some steps. For > example hydrolysis steps. I am going to estimate QM/MM reaction and > activation energy barriers for > all the steps involved. Problem is how do i include the waters for some > steps in the middle of the > reaction profile. I am going to use several MD snapshot as starting > structures, but will be striping off > waters. What about doing an MD simulation with water for the particular > structure and select some > waters around the active site. In that case the problem is how many? just > one..may be couple of more > waters bound to the particular water molecule involved?? Several shells of > water..Can anyone help me > to find journal articles on similar problems. Any citations or suggestions > are mostly welcomed. Thank > you all in advance. > > LC> > > --0016e6498a5cf6d9bc0481e29b18 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hiii
For this you can try this application Water Map from SchrodingerHere is the doi of an article using Water Map
10.1002/pro.177 (wiley i= nterscience)=A0 Title:=A0 High-energy water sites determine peptide binding= affinity and specificity of PDZ domains.

Thanks
Rocky


On Mon, Mar 15, 2= 010 at 10:50 PM, Lochana C Menikarachchi lochanac^^yahoo.com <owner-chemistry|,|ccl.net> wrote:

Sent to CCL by: "Lochana C Menikarachchi" [lochanac#,#yahoo.com]
Dear All,

I need to model an enzymatic reaction in which explicit water molecules par= ticipate in some steps. For
example hydrolysis steps. I am going to estimate QM/MM reaction and activat= ion energy barriers for
all the steps involved. Problem is how do i include the waters for some ste= ps in the middle of the
reaction profile. I am going to use several MD snapshot as starting structu= res, but will be striping off
waters. What about doing an MD simulation with water for the particular str= ucture and select some
waters around the active site. In that case the problem is how many? just o= ne..may be couple of more
waters bound to the particular water molecule involved?? Several shells of = water..Can anyone help me
to find journal articles on similar problems. Any citations or suggestions = are mostly welcomed. Thank
you all in advance.

LC



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--0016e6498a5cf6d9bc0481e29b18-- From owner-chemistry@ccl.net Tue Mar 16 01:15:01 2010 From: "Kalju Kahn kalju]~[chem.ucsb.edu" To: CCL Subject: CCL: Water molecules participating in Enzymatic Reactions Message-Id: <-41445-100316011253-23952-c0A+02B88kAoo0HagHVThg++server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 15 Mar 2010 22:12:41 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju .. chem.ucsb.edu] Lochana, As for the number of water molecules in hydrolysis, I would think that laying out few plausible mechanisms for catalysis on the paper will give you some sense of what is needed to complete all the steps in the reaction. Imagine you are hydrolyzing an amide using a mechanism in which the enzyme participates as a covalent catalyst (classical chymotrypsin example). You need to think what deprotonates your nucleophile (water or another residue?), and what stabilizes the negative charge on the oxyanion (some backbone amides, or water?) At some point the first product is leaving, but it needs to be protonated. You need to think what serves the role of acid here (some residue in the enzyme, or water). Then a water molecule comes in and rescues the enzyme from the covalent complex. Every time your answer is "water", you need to include this one to the QM region. It seems to me that you can tackle the problem step-wise and only include waters that are actively participating in each step. I would think that if you are not sure about what you are doing, start with QM/MM reaction path minimization instead of MD with a QM region. This merely gives you activation energies (not free energies) but allows you to probe possible mechanisms one at a time. You may need to keep the QM waters (partially) fixed at a reasonable position during this process or you will spend all your time minimizing the dihedral angle of the distant hydrogen of a loosely bound water molecule. As far as Rocky's answer below ... I fail to see how this is applicable. Hope this helps P.S. I cannot claim that I speak from a successful experience with a problem like yours. Kalju > Hiii > For this you can try this application Water Map from Schrodinger > Here is the doi of an article using Water Map > 10.1002/pro.177 (wiley interscience) Title: High-energy water sites > determine peptide binding affinity and specificity of PDZ domains. > > Thanks > Rocky > > > On Mon, Mar 15, 2010 at 10:50 PM, Lochana C Menikarachchi lochanac^^ > yahoo.com wrote: > >> >> Sent to CCL by: "Lochana C Menikarachchi" [lochanac#,#yahoo.com] >> Dear All, >> >> I need to model an enzymatic reaction in which explicit water molecules >> participate in some steps. For >> example hydrolysis steps. I am going to estimate QM/MM reaction and >> activation energy barriers for >> all the steps involved. Problem is how do i include the waters for some >> steps in the middle of the >> reaction profile. I am going to use several MD snapshot as starting >> structures, but will be striping off >> waters. What about doing an MD simulation with water for the particular >> structure and select some >> waters around the active site. In that case the problem is how many? >> just >> one..may be couple of more >> waters bound to the particular water molecule involved?? Several shells >> of >> water..Can anyone help me >> to find journal articles on similar problems. Any citations or >> suggestions >> are mostly welcomed. Thank >> you all in advance. >> >> LC> >> >> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Tue Mar 16 03:38:00 2010 From: "Prasenjit.Seal#%#crm2.uhp-nancy.fr" To: CCL Subject: CCL: problem on g09 Message-Id: <-41446-100316023359-24898-Vn635zLIjODI6fSDeFSUIQ*|*server.ccl.net> X-Original-From: Prasenjit.Seal a crm2.uhp-nancy.fr Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 16 Mar 2010 07:33:46 +0100 MIME-Version: 1.0 Sent to CCL by: Prasenjit.Seal%x%crm2.uhp-nancy.fr Selon "Xiaohui Kang huixiaokang328::163.com" : > > Sent to CCL by: "Xiaohui Kang" [huixiaokang328 ~~ 163.com] > Dear CCL Subscribers > When I compute the thermochemistry of water at both 298.15K and 373K in an > input file with g09,I can not get the information on 373K ,that is to say,the > "--Link--" does not play a role in my calculation.The following is my input > file : > > %Chk=watertest.chk > %nproc=8 > #T RHF/6-31G(d) Freq=noraman > water298 > > 0 1 > O 0.00000000 0.00000000 0.11980000 > H 0.00000000 0.76140000 -0.47910000 > H 0.00000000 -0.76140000 -0.47910000 > > --Link1-- > %Chk=watertest.chk > %nproc=8 > #T RHF/6-31G(d) Geom=Check Freq=ReadFC Guess=Read Test > > water373 > > 0 1 > > 373.0 1.0 0.9 > 16 > 1 > 1 > Can anybody tell me what is the reason resulting in this phenomenon? > > Sincerely > > xkang> > > Dear Prof. Kang, You can try it by writting "Temperature=373" in the route section of the second link instead of writting it in one of the bottom lines. Regards, PS From owner-chemistry@ccl.net Tue Mar 16 04:38:01 2010 From: "Laurence Leherte laurence.leherte%%fundp.ac.be" To: CCL Subject: CCL: Porous volume calculation Message-Id: <-41447-100316043512-28270-hzIxGyDCgf9yOJov+7Aikw .. server.ccl.net> X-Original-From: "Laurence Leherte" Date: Tue, 16 Mar 2010 04:35:08 -0400 Sent to CCL by: "Laurence Leherte" [laurence.leherte(0)fundp.ac.be] Dear CCL Subscribers, A colleague of mine wishes to calculate the porous volume of a compound he synthetized starting from its crystallographic coordinates. Do you know of any user-friendly and free software that might be useful to do that ? (Maybe a visualizing tool that includes calculation of interactomic distances and/or accessible volume, ...) I thank you very much in advance for your reply. With my best regards, Laurence Leherte Dept of Chemistry Laboratoire de Physico-Chimie Informatique Unite de Chimie Physique Theorique et Structurale University of Namur (Belgium) From owner-chemistry@ccl.net Tue Mar 16 06:13:01 2010 From: "Michel Petitjean petitjean.chiral]-[gmail.com" To: CCL Subject: CCL: Porous volume calculation Message-Id: <-41448-100316060556-3106-kMG4lk1MJ0xmpuVxkIcALw#%#server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 16 Mar 2010 10:35:37 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral{}gmail.com] Dear Laurence, The volume of the union of the atomic spheres may be a first step in the calculation you need. If so, please have a look to the ASV freeware: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Best regards, Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral]^[gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.spheres.html ...........................................................................= .................... Sent to CCL by: "Laurence =A0Leherte" [laurence.leherte(0)fundp.ac.be] Dear CCL Subscribers, A colleague of mine wishes to calculate the porous volume of a compound he synthetized starting from its crystallographic coordinates. =A0Do you know of any user-friendly and free software that might be useful to do that ? =A0(Maybe a visualizing tool that includes calculation of interactomic distances and/or accessible volume, ...) I thank you very much in advance for your reply. With my best regards, Laurence Leherte Dept of Chemistry Laboratoire de Physico-Chimie Informatique Unite de Chimie Physique Theorique et Structurale University of Namur (Belgium) From owner-chemistry@ccl.net Tue Mar 16 06:48:00 2010 From: "Bora Karasulu bkarasulu(0)ku.edu.tr" To: CCL Subject: CCL: Error in running CPMD on single machine with 16 cores using OpenMPI Message-Id: <-41449-100316060700-3217-I0n5Hm8VsIH6pEEkWXOe1A[a]server.ccl.net> X-Original-From: Bora Karasulu Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-9; format=flowed Date: Tue, 16 Mar 2010 11:14:32 +0200 MIME-Version: 1.0 Sent to CCL by: Bora Karasulu [bkarasulu-$-ku.edu.tr] Dear CCLers and CPMD users, I have problems using the CPMD in parallel with OpenMPI. The computer has two processors with 8 cores (an HP workstation) with 36 GB of RAM. I installed CPMD on FEDORA 12, and installed the required packages using built-in package installer of FEDORA. The problem is the following. When I run CPMD 3.13.2 OpenMPI version with mpirun command, program stops running at the beginning (after the part processors are allocated) or during the geometry/wavefunction optimizations. The job is not killed in the table of processes (top) but the program does not yield any output. I experience this problem when I use CPMD with 3 or more processors, while there is no problem with two processors. (This means the program succesfully terminates.) In addition, when I submit another 2-processor job the time required for each optimization step increases. (Processors' efficiency decreases.) I think the problem is related with the share of the memory by the processors. However, I could not find any solution in the Google-search. I really appreciate your comments about this error. Thank you very much. Bora Karasulu From owner-chemistry@ccl.net Tue Mar 16 08:45:01 2010 From: "Pierre Archirel pierre.archirel[a]u-psud.fr" To: CCL Subject: CCL:G: change temperature in gaussian 09 Message-Id: <-41450-100316084004-22130-L5xcZBonfti5evY+donZVQ+*+server.ccl.net> X-Original-From: "Pierre Archirel" Date: Tue, 16 Mar 2010 08:40:00 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel[*]u-psud.fr] This is an answer to Xiaohui Kang: There is a bug in gaussian 09 about changing temperature in the harmonic analysis. The only way of changing temperature is to use the freqchk utility. Regards. Pierre Archirel, LCP Universite Paris-Sud, Orsay, France From owner-chemistry@ccl.net Tue Mar 16 09:19:01 2010 From: "jaleel uc jaleel.uc[a]gmail.com" To: CCL Subject: CCL: Essential books in computational chemistry (drug design) Message-Id: <-41451-100316033752-29936-ZYTHldgG3BcBP2czlrZ18Q]|[server.ccl.net> X-Original-From: jaleel uc Content-Type: multipart/alternative; boundary=001636c5c07511dd160481e52b13 Date: Tue, 16 Mar 2010 12:02:56 +0530 MIME-Version: 1.0 Sent to CCL by: jaleel uc [jaleel.uc[-]gmail.com] --001636c5c07511dd160481e52b13 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable The following books are use full in beginning stage . * 1. Essentials of Computational Chemistry * Theories and Models Second Edition * Christopher J. Cramer ** Department of Chemistry and Supercomputing Institute, University of Minnesota, USA 2. medicinalchemistry patrik 3. Drug Design". Andrew Leach: * On 3/16/10, Yvonne Martin yvonnecmartin_+_gmail.com wrote: > > > Sent to CCL by: Yvonne Martin [yvonnecmartin\a/gmail.com] > The second edition of my book "Quantitative Drug Design" is in press. > I don't have a publication date, but the publisher indicates April or > May. > > Yvonne Martin > > On Mon, Mar 15, 2010 at 6:29 PM, Cyril Bauvais cyril.bauvais^u-psud.fr > wrote: > > Hi Senthil, Salut Florent > > > > this one is also very good : > > Molecular Modeling of Inorganic Compounds, 3rd Edition > > Peter Comba, Trevor W. Hambley, Bodo Martin > > ISBN: 978-3-527-31799-8 > > > http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527317996,descCd-table= OfContents.html > > > > About ADME, recent review articles should give you up to date > informations > > about it... > > > > Best, > > > > Cyril > > > > > > > > > > 2010/3/15 Barbault Florent florent.barbault*_*univ-paris-diderot.fr > > > >> > >> Sent to CCL by: "Barbault Florent" > >> [florent.barbault/./univ-paris-diderot.fr] > >> Hi, > >> > >> Personnaly, I found the book "molecular modelling: principles and > >> applications" very useful... Here is the link on amazon (I have no > interest > >> on this book!) > >> > >> > >> > http://www.amazon.com/Molecular-Modelling-Principles-Applications-2nd/dp/= 0582382106/ref=3Dsr_1_1?ie=3DUTF8&s=3Dbooks&qid=3D1268686522&sr=3D8-1 > >> > >> Best regards > >> Florent Barbault > >> > >> > >> On Mon, 15 Mar 2010 15:35:39 -0400 > >> "Senthil Natesan sen.natesan]^[yahoo.com" > >> wrote: > >>> > >>> Sent to CCL by: "Senthil Natesan" [sen.natesan,yahoo.com] > >>> Dear All, > >>> > >>> Greetings. It will be very helpful if you could recommend a few > >>> essential (authoritative in its area) books in the following areas > >>> > >>> 1) Molecular dynamics simulation > >>> 2) Molecular recognition > >>> 3) QM/MM calculations > >>> 4) QSAR > >>> 5) ADMET > >>> > >>> Books published after 2000 would be great as it would cover the lates= t > >>> developments. > >>> > >>> Thanks everyone for your time and valuable recommendations. > >>> > >>> Senthil Natesan, > >>> > >>> > >>> > >>> -=3D This is automatically added to each message by the mailing scrip= t =3D- > >>> http://server.ccl.net/chemistry/announcements/conferences/> > >> > >> ------------------------------------------------- > >> Dr Florent Barbault > >> Maitre de conferences / Assistant professor > >> > >> Universite Paris Diderot > >> Laboratoire ITODYS > >> 15 rue Jean de Ba=C4=BCf, b=C4=81timent Lavoisier > >> 75013 Paris FRANCE > >> http://www.itodys.univ-paris7.fr/ > >> tel : (33) 01-57-27-88-50 > >> e-mail : florent.barbault=3Duniv-paris-diderot.fr > >> ------------------------------------------------- > >> > >> > >> > >> -=3D This is automatically added to each message by the mailing script= =3D- > >> E-mail to subscribers: CHEMISTRY]*[ccl.net or use: > >> >> > >> E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net or use > >> Conferences: > >> http://server.ccl.net/chemistry/announcements/conferences/>> >> > >> > > > > > > > > - This is automatically added to each message by the mailing script -> > > --=20 Dr U.C.A.Jaleel. lecturer in cheminformatics Malabar christian college calicut --001636c5c07511dd160481e52b13 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
The following books are use full in beginning stage .
=C2=A0

1. Essentials of Computational Chemistry=

Theories and Models

Second Edition

Christopher J. Cramer

<= /b>

Department of Chemistry and Supercomputi= ng Institute,

University of Minnesota, USA

2. medicinalchemistry=C2=A0 patrik

3. Drug Design". Andrew Leach:

=C2=A0

=C2=A0

=C2=A0

=C2=A0
On 3/16/10, = Yvonne Martin yvonnecmartin_+_gmail.com <owner-chemistry-$-ccl.net> wrote:

Sent to CCL by: Yvonne Marti= n [yvonnecmartin\a/gmail.com]
The secon= d edition of my book "Quantitative Drug Design" is in press.
I don't have a publication date, but the publisher indicates April orMay.

Yvonne Martin

On Mon, Mar 15, 2010 at 6:29 PM, Cyril B= auvais cyril.bauvais^u-psud.fr
<owne= r-chemistry:+:ccl.net> wrote:
> Hi Senthil, Salut Florent
>
> this one is also very good :=
> Molecular Modeling of Inorganic Compounds, 3rd Edition
> Pet= er Comba, Trevor W. Hambley, Bodo Martin
> ISBN: 978-3-527-31799-8 > http://eu.wiley.com/WileyCDA/WileyTitle/prod= uctCd-3527317996,descCd-tableOfContents.html
>
> About ADME= , recent review articles should give you up to date informations
> about it...
>
> Best,
>
> Cyril
>
>= ;
>
>
> 2010/3/15 Barbault Florent florent.barbault*_*univ-paris-diderot.fr
> <= ;owner-chemistry]*[ccl.net>
>>
>> Sent to CCL by: "Barbault Florent"
>&g= t; [florent.barbault/./univ-paris-= diderot.fr]
>> Hi,
>>
>> Personnaly, I found= the book "molecular modelling: principles and
>> applications" very useful... Here is the link on amazon (I ha= ve no interest
>> on this book!)
>>
>>
>&g= t; http://www.amazon.com/Molecular-Modelling-Principles-Ap= plications-2nd/dp/0582382106/ref=3Dsr_1_1?ie=3DUTF8&s=3Dbooks&qid= =3D1268686522&sr=3D8-1
>>
>> Best regards
>> Florent Barbault
>><= br>>>
>> On Mon, 15 Mar 2010 15:35:39 -0400
>>=C2= =A0=C2=A0"Senthil Natesan sen.natesan]^[y= ahoo.com" <owner-chemistry=3Dccl.net= >
>> wrote:
>>>
>>> Sent to CCL by: "Senth= il=C2=A0=C2=A0 Natesan" [sen.natesan,yaho= o.com]
>>> Dear All,
>>>
>>> Greeti= ngs. It will be very helpful=C2=A0=C2=A0if you could recommend a few
>>> essential (authoritative in its area) books in the following a= reas
>>>
>>> 1) Molecular dynamics simulation
&g= t;>> 2) Molecular recognition
>>> 3) QM/MM calculations >>> 4) QSAR
>>> 5) ADMET
>>>
>>&g= t; Books published after 2000 would be great as it would cover the latest>>> developments.
>>>
>>> Thanks everyon= e for your time and valuable recommendations.
>>>
>>> Senthil Natesan,
>>>
>>&g= t;
>>>
>>> -=3D This is automatically added to each= message by the mailing script =3D-
>>> http://server.ccl.net/chemi= stry/announcements/conferences/>
>>
>> -------------------------------------------------
&= gt;> Dr Florent Barbault
>> Maitre de conferences / Assistant p= rofessor
>>
>> Universite Paris Diderot
>> Labor= atoire ITODYS
>> 15 rue Jean de Ba=C4=BCf, b=C4=81timent Lavoisier
>> 7501= 3 Paris FRANCE
>> ht= tp://www.itodys.univ-paris7.fr/
>> tel=C2=A0=C2=A0: (33) 01-57= -27-88-50
>> e-mail : florent.barbault=3Duniv-paris-diderot.fr
>> -------------------------------------------------
>>
&= gt;>
>>
>> -=3D This is automatically added to each me= ssage by the mailing script =3D-
>> E-mail to subscribers: CHEMIST= RY]*[ccl.net or use:
>>=C2=A0=C2=A0=C2=A0=C2=A0>>
>> E-mail to administrato= rs: CHEMISTRY-REQUEST]*[ccl.net or use
&g= t;>=C2=A0=C2=A0=C2=A0=C2=A0Conferences:
>> http://server.ccl.net/ch= emistry/announcements/conferences/>>=C2=A0=C2=A0=C2=A0=C2=A0>&= gt;
>>
>
>



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--
Dr U.C.A.Jaleel.
lecturer in = cheminformatics
Malabar christian college
calicut=20 --001636c5c07511dd160481e52b13-- From owner-chemistry@ccl.net Tue Mar 16 09:56:00 2010 From: "Chris Perry christopher.perry2#%#wits.ac.za" To: CCL Subject: CCL:G: Gaussian03/09 and Infiniband Message-Id: <-41452-100316044830-4327-fbiJ8S24KCoLl+21ZxNysg##server.ccl.net> X-Original-From: "Chris Perry" Date: Tue, 16 Mar 2010 04:48:26 -0400 Sent to CCL by: "Chris Perry" [christopher.perry2===wits.ac.za] Dear colleagues We have have built a small cluster of computers that run G03 and G09 under Linux. Currently we are using standard 1-gigabit ethernet networking to interconnect the nodes, but are looking to upgrad this. A bit of research on the net has revealed that Infiniband seems to be the way to go. My question is does Gaussian (or rather TCP-Linda) support Infiniband? Would I need to obtain new G03/G09 binaries to get the networking to work, or would it be handled naitively by the operating system? Thanks in advance Chris Christopher B. Perry, PhD Lecturer, School of Chemistry University of the Witwatersrand PO Wits, Johannesburg 2050, South Africa Tel +27 +11 717 6732 Fax +27 +11 717 6749 Email: Christopher.Perry2[#]wits.ac.za From owner-chemistry@ccl.net Tue Mar 16 10:29:00 2010 From: "Mira Cuperlovic-Culf cuperlovim ~ nrc.ca" To: CCL Subject: CCL:G: Gauss09W install problems Message-Id: <-41453-100316091456-4940-EYzDy1PlYpuGoNN37fB/BA * server.ccl.net> X-Original-From: "Mira Cuperlovic-Culf" Date: Tue, 16 Mar 2010 09:14:53 -0400 Sent to CCL by: "Mira Cuperlovic-Culf" [cuperlovim=nrc.ca] Dear All, I have been using Gaussian for some time and love the QChem part of the software. However I had more than poor treatment from Gaussian Inc. on every level most importantly regarding software installation. with G03 I have made a mistake to get a Windows version and try to install it on 64Bit computer. This in the end was proven impossible and I had to switch to 32 bit. Once again there were many installation problems but finally, mostly through trial and error we got it on. Now I got the Gauss09W and once again it doesn't install and Gaussian tech support ignores our requests for help. So I have several questions - Do other users of Gaussian from Canada or from Government institutions or ... have such experience with Tech support from Gaussian Inc.; - Any ideas/suggestions on how to install Gauss09W on Windows 64Bit and/or 32Bit. Thank you very much for your help and info. Sincerely, Mira Cuperlovic-Culf, National Research Council of Canada, Moncton, NB, Canada From owner-chemistry@ccl.net Tue Mar 16 11:08:01 2010 From: "J r my Besnard j10b84..hotmail.com" To: CCL Subject: CCL: Essential books in computational chemistry (drug design) Message-Id: <-41454-100316105004-20836-PiUtB0nmu9GwcB6mPcZufw ~~ server.ccl.net> X-Original-From: "J r my Besnard" Date: Tue, 16 Mar 2010 10:50:00 -0400 Sent to CCL by: "J r my Besnard" [j10b84:hotmail.com] Hi, A small book I found very usefull and rich in info: An introduction to Chemoinformartics > From Andrew Leach and Valerie Gillet Also you can have a look to quite a lots of books via googlebook preview system. Cheers, Jrmy Besnard PhD student, Univerity of Dundee From owner-chemistry@ccl.net Tue Mar 16 11:40:00 2010 From: "=?ISO-8859-15?Q?Horacio_P=E9rez-S=E1nchez?= horacio.sanchez ~~ kit.edu" To: CCL Subject: CCL: Essential books in computational chemistry (drug design) Message-Id: <-41455-100316051822-19572-G2JX8K8FaARCqplpaRFCnw|server.ccl.net> X-Original-From: =?ISO-8859-15?Q?Horacio_P=E9rez-S=E1nchez?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 16 Mar 2010 09:35:24 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-15?Q?Horacio_P=E9rez-S=E1nchez?= [horacio.sanchez|-|kit.edu] Hi, related with essential books about Drug Design, I would recommend "Protein-Ligand Interactions: From Molecular Recognition to Drug Design" Regards Horacio Am 15/Mar/10 8:35 PM, schrieb Senthil Natesan sen.natesan]^[yahoo.com: > Sent to CCL by: "Senthil Natesan" [sen.natesan,yahoo.com] > Dear All, > > Greetings. It will be very helpful if you could recommend a few essential (authoritative in its area) books in the following areas > > 1) Molecular dynamics simulation > 2) Molecular recognition > 3) QM/MM calculations > 4) QSAR > 5) ADMET > > Books published after 2000 would be great as it would cover the latest developments. > > Thanks everyone for your time and valuable recommendations. > > Senthil Natesan,> > > > -- ====================================================== Dr. Horacio Pérez-Sánchez Karlsruhe Institute of Technology Institut für Nanotechnologie, Building 640-Room 223 Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany Tel: + 49 724 782 6884 Fax: + 49 724 782 6368 horacio.sanchez-x-kit.edu http://www.kit.edu http://www.research.kit.edu/biostruct/index.php ====================================================== (Message transmitted on 100% recycled electrons) From owner-chemistry@ccl.net Tue Mar 16 12:58:00 2010 From: "Mr. Satyajit Sarmah satyacs{=}tezu.ernet.in" To: CCL Subject: CCL:G: input to generate wave function file Message-Id: <-41456-100315103406-25268-bC93tMjzFu/L3kiT0DKIDg##server.ccl.net> X-Original-From: "Mr. Satyajit Sarmah" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 15 Mar 2010 19:18:36 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Mr. Satyajit Sarmah" [satyacs|a|tezu.ernet.in] Hi everyone I am using Gaussian 03 . I wanted know the required input to generate wave function file using Gaussian03. If anybody can give solution in this regard. Thanks. Satyajit. ___________________ D I S C L A I M E R This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. From owner-chemistry@ccl.net Tue Mar 16 13:34:01 2010 From: "zoran matovic zmatovic,+,kg.ac.rs" To: CCL Subject: CCL:G: Gaussian03/09 and Infiniband Message-Id: <-41457-100316112703-7431-16wVILViOUP8pmZScsGJ0g|-|server.ccl.net> X-Original-From: "zoran matovic" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 16 Mar 2010 16:26:48 +0100 MIME-Version: 1.0 Sent to CCL by: "zoran matovic" [zmatovic/a\kg.ac.rs] Dear Chris I do not think that hardware has any matter with gaussian or tcp linda. However others may help more. zoran ----- Original Message ----- > From: "Chris Perry christopher.perry2#%#wits.ac.za" To: "Matovic, Zoran D " Sent: Tuesday, March 16, 2010 9:48 AM Subject: CCL:G: Gaussian03/09 and Infiniband > > Sent to CCL by: "Chris Perry" [christopher.perry2===wits.ac.za] > Dear colleagues > > We have have built a small cluster of computers that run G03 and G09 under > Linux. Currently we are using standard 1-gigabit ethernet networking to > interconnect the nodes, but are looking to upgrad this. A bit of research > on the net has revealed that Infiniband seems to be the way to go. My > question is does Gaussian (or rather TCP-Linda) support Infiniband? Would > I need to obtain new G03/G09 binaries to get the networking to work, or > would it be handled naitively by the operating system? > > > Thanks in advance > Chris > > Christopher B. Perry, PhD > Lecturer, School of Chemistry > University of the Witwatersrand > PO Wits, Johannesburg > 2050, South Africa > > Tel +27 +11 717 6732 > Fax +27 +11 717 6749 > Email: Christopher.Perry2:_:wits.ac.za> -------------------------------------------------------------------------------- No virus found in this incoming message. Checked by AVG - www.avg.com Version: 9.0.790 / Virus Database: 271.1.1/2749 - Release Date: 03/15/10 20:33:00 From owner-chemistry@ccl.net Tue Mar 16 14:08:00 2010 From: "zoran matovic zmatovic^kg.ac.rs" To: CCL Subject: CCL:G: Gauss09W install problems Message-Id: <-41458-100316112403-3037-gtvYJwapujSrFo5NB0D/7w()server.ccl.net> X-Original-From: "zoran matovic" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 16 Mar 2010 16:23:45 +0100 MIME-Version: 1.0 Sent to CCL by: "zoran matovic" [zmatovic*o*kg.ac.rs] Hello Miro, It is out of quest problems with g09W installation. Have You got installation files? If so I do not see any problem to install gaussian on every windows 64 or 32 bit system. Anyway, whats the problem in installation? The linux installation of binaries are also pretty strightforward (except You purchased sourcecode). Regards zoran ----- Original Message ----- > From: "Mira Cuperlovic-Culf cuperlovim ~ nrc.ca" To: "Matovic, Zoran D " Sent: Tuesday, March 16, 2010 2:14 PM Subject: CCL:G: Gauss09W install problems > > Sent to CCL by: "Mira Cuperlovic-Culf" [cuperlovim=nrc.ca] > Dear All, > I have been using Gaussian for some time and love the QChem part of the > software. However I had more than poor treatment from Gaussian Inc. on > every level most importantly regarding software installation. with G03 I > have made a mistake to get a Windows version and try to install it on > 64Bit computer. This in the end was proven impossible and I had to switch > to 32 bit. Once again there were many installation problems but finally, > mostly through trial and error we got it on. Now I got the Gauss09W and > once again it doesn't install and Gaussian tech support ignores our > requests for help. So I have several questions > - Do other users of Gaussian from Canada or from Government institutions > or ... have such experience with Tech support from Gaussian Inc.; > - Any ideas/suggestions on how to install Gauss09W on Windows 64Bit and/or > 32Bit. > Thank you very much for your help and info. > Sincerely, > Mira Cuperlovic-Culf, > National Research Council of Canada, > Moncton, NB, Canada> -------------------------------------------------------------------------------- No virus found in this incoming message. Checked by AVG - www.avg.com Version: 9.0.790 / Virus Database: 271.1.1/2749 - Release Date: 03/15/10 20:33:00 From owner-chemistry@ccl.net Tue Mar 16 20:06:00 2010 From: "John McKelvey jmmckel*gmail.com" To: CCL Subject: CCL: "Fork" and "Wait" commands.. Message-Id: <-41459-100316173426-304-ftt05wRCgZlsCLnZiESSCQ..server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 16 Mar 2010 16:49:15 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel*_*gmail.com] Folks, Does anyone know of any Linux fortran compilers that have both the "wait" and "fork" commands? Thanks, John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel(~)gmail.com From owner-chemistry@ccl.net Tue Mar 16 20:41:01 2010 From: "aa aa{}chemaxon.hu" To: CCL Subject: CCL: Program announcement and call for participants: ChemAxon's 2010 E UGM: May 19-20, Budapest, Hungary Message-Id: <-41460-100316083333-21381-B3NBcWbz8mxnSOEpBNuh6w,server.ccl.net> X-Original-From: aa Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=ISO-8859-1 Date: Tue, 16 Mar 2010 12:40:04 +0100 MIME-Version: 1.0 Sent to CCL by: aa [aa*o*chemaxon.hu] Please excuse cross postings.

The program is now available for ChemAxon's 2010 European User Group Meeting being held on Wednesday and Thursday, May 19-20 at the Danubius Hotel Gellert, Budapest, Hungary. The meeting is preceded by a training day on May 18th and followed by a Markush Forum on the morning of May 21st.

Program: http://www.chemaxon.com/events/2010-eugm/#1

The meeting will feature presentations from ChemAxon users, introduce a focus session on SharePoint, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments.

Preceding the meeting will be a dual track developer and end user Training Day on May 18th. To see the topics and schedule visit:
Developer Training Day: http://www.chemaxon.com/events/2010-eugm/#3
End user: Application Focus Training Day: http://www.chemaxon.com/events/2010-eugm/#2

Following the UGM we have the first meeting of the Markush Forum, an open morning for interested organizations (users and content developers) to participate in the further development of ChemAxon’s tools for Markush structure enumeration and search. More information here: http://www.chemaxon.com/events/2010-eugm/#4

To find out more about the meeting , register or submit a poster abstract (open until May 1st) and view the program, please visit: http://www.chemaxon.com/events/2010-eugm/. To review the archives of previous meetings, including original presentations (slides and video) and meeting reports from Yvonne Martin and Wendy Warr visit: http://www.chemaxon.com/library/ugm-presentations/

We look forward to seeing you here.

BR
Alex

Selected presentations:
* Instant JChem to link chemistry and biology data.  Ian Berry.  Evotec (UK) Ltd
* Cheminformatics and SharePoint: A Big Pharma Perspective.  Luke Bullard.  Pfizer
* The Mobile Kinome.  Steven Muskal.  Eidogen
* Virtual library generation using KNIME.  Timea Polgar. ChemAxon
* Tautomerism in chemical information management systems.  Wendy A Warr.  Wendy Warr & Associates
* Implementation of ChemAxon in a SOA environment. Shane Weaver. GlaxoSmithKline
* Structure-based approaches to the indexing and retrieval of patent chemistry.  TBA.  Thomson Reuters

ChemAxon Partners participants (tbc) - see partner listing here: http://www.chemaxon.com/partners/integrators.html
--
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037, Hungary
Tel: +361 453 0435
skype: alex_allardyce
From owner-chemistry@ccl.net Tue Mar 16 21:16:00 2010 From: "Adel El-Azhary azhary[-]ksu.edu.sa" To: CCL Subject: CCL:G: unix based workstation Message-Id: <-41461-100316165724-12652-Qi/15h0q537V5ifM5IZkKA#server.ccl.net> X-Original-From: "Adel El-Azhary" Date: Tue, 16 Mar 2010 16:57:19 -0400 Sent to CCL by: "Adel El-Azhary" [azhary ~ ksu.edu.sa] Dear All: We are interested to buy a UNIX based workstation or server in the price range of $8-20k mainly to run Gaussian jobs. Any informations on what brand or a model to buy with approximate price are greatly appreciated. Best regards, Adel El-Azhary From owner-chemistry@ccl.net Tue Mar 16 21:50:01 2010 From: "nahren mascarenhas meetnahren ~ yahoo.com" To: CCL Subject: CCL: Monomer to Trimer Message-Id: <-41462-100316213529-28578-yF4m9TLwGTVxRbUYOvFdsw]*[server.ccl.net> X-Original-From: "nahren mascarenhas" Date: Tue, 16 Mar 2010 21:35:25 -0400 Sent to CCL by: "nahren mascarenhas" [meetnahren..yahoo.com] Dear CCL users, I have a trimer pfMIF,which is deposited as a monomer in PDB (ID 2WKF). Now how should I generate the coordinates to get the trimer. Thank you. Warm regards, nahren