From owner-chemistry@ccl.net Fri May 18 06:47:01 2007 From: "Herbert Fruchtl herbert.fruchtl:-:st-andrews.ac.uk" To: CCL Subject: CCL:G: cubegen for laplacian (G03) Message-Id: <-34296-070518062207-26238-1NZwHioIRXlSkqcjZVBJMQ^_^server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 18 May 2007 11:21:36 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl|-|st-andrews.ac.uk] Dear all, I would like to calculate the gradient or Laplacian of the density from a Gaussian checkpoint file. This is what I tried: > cubegen 0 laplacian water.fchk lap.cube What=LAPLACIAN Unrecognized command in CubeGen. > cubegen 0 potential=laplacian water.fchk lap.cube Could not find Total LAPLACIAN Density on formatted checkpoint file. What am I doing wrong? Do I need to specify a keyword in the Gaussian input (AIM doesn't help). Thanks in advance, Herbert -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Fri May 18 07:51:00 2007 From: "Adlane sayede adlane.sayede]~[gmail.com" To: CCL Subject: CCL:G: restart of frequency jobs Message-Id: <-34297-070518040949-8574-zAtfsLsAXu3fKNehdoFjMw###server.ccl.net> X-Original-From: "Adlane sayede" Content-Type: multipart/alternative; boundary="----=_Part_21172_7641605.1179472333752" Date: Fri, 18 May 2007 09:12:13 +0200 MIME-Version: 1.0 Sent to CCL by: "Adlane sayede" [adlane.sayede],[gmail.com] ------=_Part_21172_7641605.1179472333752 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi everybody, Is it possible to take back (restart) a frequency job on Gaussian 03 calculation? Unfortunately I am running under queuing system which not allow jobs grater than 24 hours!!!! Thank you for your help, Adlane ------=_Part_21172_7641605.1179472333752 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

Hi everybody,

 

Is it possible to take back (restart) a frequency job on Gaussian 03 calculation?

Unfortunately I am running under queuing system which not allow jobs grater than 24 hours!!!!

 

Thank you for your help,

 

Adlane

------=_Part_21172_7641605.1179472333752-- From owner-chemistry@ccl.net Fri May 18 09:23:01 2007 From: "Barbara Jagoda-Cwiklik barbara.cwiklik . uochb.cas.cz" To: CCL Subject: CCL:G: restart of frequency jobs Message-Id: <-34298-070518090322-26613-ytYN9rCGH/VvO0KHajJZhA{=}server.ccl.net> X-Original-From: "Barbara Jagoda-Cwiklik" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 18 May 2007 15:03:17 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Barbara Jagoda-Cwiklik" [barbara.cwiklik-,-uochb.cas.cz] Hi Adlane, Yes, it is. You need a checkpoint file: http://www.ccl.net/cca/documents/dyoung/topics-orig/checkpoint.html then you can restart a job using previously generated checkpoint and Freq=Restart keyword. Best, Basia -- Barbara Jagoda-Cwiklik, Ph.D Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Prague, Czech Republic e-mail: barbara.cwiklik%uochb.cas.cz > Hi everybody, > > Is it possible to take back (restart) a frequency job on Gaussian 03 > calculation? > > Unfortunately I am running under queuing system which not allow jobs > grater > than 24 hours!!!! > > > > Thank you for your help, > > > > Adlane From owner-chemistry@ccl.net Fri May 18 11:50:00 2007 From: "Sergio Emanuel Galembeck segalemb . usp.br" To: CCL Subject: CCL:G: restart of frequency jobs Message-Id: <-34299-070518091623-27584-s6+p1fC1wbMPMvr+t8SAow:_:server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 18 May 2007 09:15:56 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb|a|usp.br] Dear Adlane, No it isn't possible to restart frequency calculations. You need to talk to system administrator. Best regards, Sergio Galembeck Citando "Adlane sayede adlane.sayede]~[gmail.com" : > Hi everybody, > > > > Is it possible to take back (restart) a frequency job on Gaussian 03 > calculation? > > Unfortunately I am running under queuing system which not allow jobs grater > than 24 hours!!!! > > > > Thank you for your help, > > > > Adlane From owner-chemistry@ccl.net Fri May 18 12:25:00 2007 From: "Jian computationalboy%a%gmail.com" To: CCL Subject: CCL: Volume of active site in protein Message-Id: <-34300-070518111754-30441-uOWDocxg9r0n7dZFHIIIsw!A!server.ccl.net> X-Original-From: Jian Content-Type: multipart/alternative; boundary="----=_Part_28405_26842800.1179501024546" Date: Fri, 18 May 2007 23:10:24 +0800 MIME-Version: 1.0 Sent to CCL by: Jian [computationalboy]|[gmail.com] ------=_Part_28405_26842800.1179501024546 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Have you tried Voidoo? It is a freeware that can calculate the volume of protein active sites. However, I have no idea how to visulizase its results. O was used in the tutorial, but I don't know how to attain it. Besides, siteID in Sybyl is useful for your problem. Regards! Jian On 5/9/07, rafi A rafi4dd]|[gmail.com wrote: > > > Sent to CCL by: "rafi A" [rafi4dd(a)gmail.com] > Hello everyone, > > Is there any method or software to know the volume of the protein active > site or the volume of a particular cavity in protein. > > Thank you > > Rafi> > > > ------=_Part_28405_26842800.1179501024546 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Have you tried Voidoo?
It is a freeware that can calculate the volume of protein active sites.
However, I have no idea how to visulizase its results. O was used in the tutorial, but I don't know how to attain it.
Besides, siteID in Sybyl is useful for your problem.
Regards!
Jian


 
On 5/9/07, rafi A rafi4dd]|[gmail.com <owner-chemistry%%ccl.net> wrote:

Sent to CCL by: "rafi  A" [rafi4dd(a)gmail.com]
Hello everyone,

Is there any method or software to know the volume of the protein active site or the volume of a particular cavity in protein.

Thank you

Rafi



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------=_Part_28405_26842800.1179501024546-- From owner-chemistry@ccl.net Fri May 18 13:04:01 2007 From: "Daria Khvostichenko dkhvosti(_)uiuc.edu" To: CCL Subject: CCL: restart of frequency jobs Message-Id: <-34301-070518125504-8505-6R59eHo5yTuc1cnzptpaTg]|[server.ccl.net> X-Original-From: "Daria Khvostichenko" Date: Fri, 18 May 2007 12:55:00 -0400 Sent to CCL by: "Daria Khvostichenko" [dkhvosti-,-uiuc.edu] Hello, Yes, you can restart NUMERICAL frequency jobs: the keyword is freq=numer for the first job and freq=(numer,restart) for restarts. Numerical fequency jobs usually take longer that analytical; they perform 6*(number of atoms) SCF calculations. You may want to run both on a smaller system to check how the two compare in terms of results (frequencies, etc.) Daria From owner-chemistry@ccl.net Fri May 18 13:35:01 2007 From: "Andrew Joseph Adamczyk a-adamczyk---northwestern.edu" To: CCL Subject: CCL:G: Defining quadrupole in Gaussian 03 Message-Id: <-34302-070518131259-23069-XaIfD05ozq7VN1FcwXffMg++server.ccl.net> X-Original-From: "Andrew Joseph Adamczyk" Date: Fri, 18 May 2007 13:12:56 -0400 Sent to CCL by: "Andrew Joseph Adamczyk" [a-adamczyk]=[northwestern.edu] Hello Everyone, Ultimately I want to assign the charges for the quadrupole moment in N2 against the bias in Gaussian described below (or perhaps persuade against the bias). That is, I am able to generate the quadrupole tensor which has nonzero components Qxx, Qyy, and Qzz. The latter of which is the calculated quadrupole moment for N2. This is with the bias that the quadrupole is of -++- conformation. I also ran the pop=chelpg option and received the following output which only constrains the dipole moment giving zero partial charges: Breneman (CHELPG) radii used. Generate Potential Derived Charges using the Breneman model, NDens= 1. Grid spacing= 0.300 Box extension= 2.800 NStep X,Y,Z= 20 20 24 Total possible points= 9600 Number of Points to Fit= 3328 ********************************************************************** Electrostatic Properties Using The SCF Density ********************************************************************** Atomic Center 1 is at 0.000000 0.000000 0.554640 Atomic Center 2 is at 0.000000 0.000000 -0.554640 3328 points will be used for fitting atomic charges Fitting point charges to eletrostatic potential Charges from ESP fit, RMS= 0.00536 RRMS= 1.00000: Charge= 0.00000 Dipole= 0.0000 0.0000 0.0000 Tot= 0.0000 1 1 N 0.000000 2 N 0.000000 If anyone is able to manipulate Gaussian to allow for unique quadrupole arrangements (with point charges perhaps) in an effort to generate the electrostatic potential surface, your suggestions would be greatly appreciated. Thank you in advance. From owner-chemistry@ccl.net Fri May 18 14:13:00 2007 From: "Dorothee Berthomieu bertho~!~univ-montp2.fr" To: CCL Subject: CCL:G: restart of frequency jobs Message-Id: <-34303-070518123458-28730-eTz3EEaR9FkOxaQRaaHXAA#%#server.ccl.net> X-Original-From: Dorothee Berthomieu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 18 May 2007 17:34:46 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Dorothee Berthomieu [bertho{=}univ-montp2.fr] Hi You can restart frequency calculations, but only numerical frequency calculations. key word with gaussian : Freq(Numer,restart) Best regards Dr. Dorothee Berthomieu ************************************************** MACS (Laboratoire des Materiaux Avances pour la Catalyse et la Sante) Institut Charles Gerhardt UMR 5253 CNRS/ENSCM/UM2/UM1 Ecole Nationale Superieure de Chimie de Montpellier 8, rue de l'Ecole Normale 34296 MONTPELLIER cedex 5 FRANCE Tel : 33 (0) 467 163 473 Telecopie : 33 (0) 467 163 470 email : bertho%univ-montp2.fr www.icg.univ-montp2.fr On Fri, 18 May 2007, Barbara Jagoda-Cwiklik barbara.cwiklik . uochb.cas.cz wrote: > > Sent to CCL by: "Barbara Jagoda-Cwiklik" [barbara.cwiklik-,-uochb.cas.cz] > Hi Adlane, > > Yes, it is. You need a checkpoint file: > http://www.ccl.net/cca/documents/dyoung/topics-orig/checkpoint.html > then you can restart a job using previously generated checkpoint and > Freq=Restart keyword. > > Best, > Basia > > > -- > Barbara Jagoda-Cwiklik, Ph.D > Center for Biomolecules and Complex Molecular Systems > Institute of Organic Chemistry and Biochemistry, > Academy of Sciences of the Czech Republic > Prague, Czech Republic > e-mail: barbara.cwiklik~~uochb.cas.cz > > >> Hi everybody, >> >> Is it possible to take back (restart) a frequency job on Gaussian 03 >> calculation? >> >> Unfortunately I am running under queuing system which not allow jobs >> grater >> than 24 hours!!!! >> >> >> >> Thank you for your help, >> >> >> >> Adlane> > > > From owner-chemistry@ccl.net Fri May 18 14:48:00 2007 From: "Joe Leonard jleonard42{=}gmail.com" To: CCL Subject: CCL: Computer History Museum Message-Id: <-34304-070518140455-27129-c0A+02B88kAoo0HagHVThg:server.ccl.net> X-Original-From: Joe Leonard Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 18 May 2007 13:02:44 -0400 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Joe Leonard [jleonard42^_^gmail.com] Folks, as many groups (both academic and commercial) have used computers over the years, I wanted to pass along the website for the Computer History Museum: http://www.computerhistory.org/ We visited this last month, and I was surprised by the number of machines that I've worked on at some point! If anybody has old machines that they're getting rid of that they think might be of "historical value", why not get in contact with them to see whether they'd like it in their collection. Nothing might come of it, but there's been a LOT of iron used by the QM folks, for example, that might be of interest. Non-machine material might also be of value - early calculations, things done by Laureats, etc. In some ways, we've been willing to forget our past more easily than other disciplines, and perhaps organizations like the museum might change that in some small way. FYI Joe Leonard jleonard42]-[gmail.com From owner-chemistry@ccl.net Fri May 18 20:08:00 2007 From: "Ted Cabeen cabeen{:}chem.ucsb.edu" To: CCL Subject: CCL: Computer History Museum Message-Id: <-34305-070518183442-13240-XoD/hx10ws1Pgm8iiiAYnw(!)server.ccl.net> X-Original-From: Ted Cabeen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 18 May 2007 14:54:44 -0700 MIME-Version: 1.0 Sent to CCL by: Ted Cabeen [cabeen]^[chem.ucsb.edu] Joe Leonard jleonard42{=}gmail.com wrote: > Folks, as many groups (both academic and commercial) have used computers > over the years, I wanted to pass along the website for the Computer > History Museum: > > http://www.computerhistory.org/ > > We visited this last month, and I was surprised by the number of > machines that I've worked on at some point! If anybody has old machines > that they're getting rid of that they think might be of "historical > value", why not get in contact with them to see whether they'd like it > in their collection. Nothing might come of it, but there's been a LOT > of iron used by the QM folks, for example, that might be of interest. > Non-machine material might also be of value - early calculations, things > done by Laureats, etc. > > In some ways, we've been willing to forget our past more easily than > other disciplines, and perhaps organizations like the museum might > change that in some small way. If you are considering giving items, I'd make sure that you've looked at the "No Longer Accepting" list, as there are quite a few things they already have: http://www.computerhistory.org/collections/donateArtifact/dnw.php If you have something that they might want, here's the general page on giving computing artifacts: http://www.computerhistory.org/collections/donateArtifact/ --Ted From owner-chemistry@ccl.net Fri May 18 21:26:01 2007 From: "Jian computationalboy|*|gmail.com" To: CCL Subject: CCL: Conformation search with Monte Carlo method Message-Id: <-34306-070518111814-30502-yhdQNg4IxEhWVa6CEtgGMg::server.ccl.net> X-Original-From: Jian Content-Type: multipart/alternative; boundary="----=_Part_28473_1925085.1179501486072" Date: Fri, 18 May 2007 23:18:06 +0800 MIME-Version: 1.0 Sent to CCL by: Jian [computationalboy * gmail.com] ------=_Part_28473_1925085.1179501486072 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, everyone: I am trying to find the global stable conformation of a complex structure. Systematic search did not work due to too many rotable bonds. So I want to try Monte Carlo method. Can any one tell me how to apply this method and is there any free software to run? I will be greatly appreciate your help! Jian ------=_Part_28473_1925085.1179501486072 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hello, everyone:
I am trying to find the global stable conformation of a complex structure.
Systematic search did not work due to too many rotable bonds.
So I want to try Monte Carlo method.
Can any one tell me how to apply this method and is there any free software to run? 
I will be greatly appreciate your help!
 
Jian
------=_Part_28473_1925085.1179501486072-- From owner-chemistry@ccl.net Fri May 18 22:32:01 2007 From: "Jian computationalboy+*+gmail.com" To: CCL Subject: CCL: query regarding Zdock/Rdock Message-Id: <-34307-070518222743-14050-UNx87URgxW7cVfCZQnK2iA++server.ccl.net> X-Original-From: Jian Content-Type: multipart/alternative; boundary="----=_Part_32721_26295278.1179541657144" Date: Sat, 19 May 2007 10:27:37 +0800 MIME-Version: 1.0 Sent to CCL by: Jian [computationalboy#%#gmail.com] ------=_Part_32721_26295278.1179541657144 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline ZDOCK has become a part in InsightII, however, it is still free for academic researcher. Install ZDOCK was quite easy, in my mind. I download the tar file, and extract the files into /usr/local/zdock2.3 directory. Then define the PATH, and when I typed $which zdock The zdock path displayed. I think it can work. Through I have not performed docking yet. Regards! On 5/8/07, Kalyan chaitanya kalyanpulipaka _ gmail.com < owner-chemistry|a|ccl.net> wrote: > > Dear all > > i have recently started protein-protein docking and likely to get started > with Zdock/Rdock, but iam facing a challenge regarding the installation of > the same software, is there any one who is working on this and help me.... > > Thankyou in advance, > > Regards, > > P.Kalyan > ------=_Part_32721_26295278.1179541657144 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline ZDOCK has become a part in InsightII, however, it is still free for academic researcher.
Install ZDOCK was quite easy, in my mind.
I download the tar file, and extract the files into /usr/local/zdock2.3 directory. Then define the PATH, and when I typed
$which zdock
The zdock path displayed.
I think it can work.
Through I have not performed docking yet.
Regards!

On 5/8/07, Kalyan chaitanya kalyanpulipaka _ gmail.com <owner-chemistry|a|ccl.net> wrote:
Dear all

i have recently started protein-protein docking and likely to get started with Zdock/Rdock, but iam facing a challenge regarding the installation of the same software, is there any one who is working on this and help me....

Thankyou in advance,

Regards,

P.Kalyan

------=_Part_32721_26295278.1179541657144-- From owner-chemistry@ccl.net Fri May 18 23:08:00 2007 From: "huanglei huanglei=mail.utexas.edu" To: CCL Subject: CCL: Conformation search with Monte Carlo method Message-Id: <-34308-070518230013-28958-rd8ELvMq2lQkuN0FHuevVQ/./server.ccl.net> X-Original-From: "huanglei" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Fri, 18 May 2007 21:23:45 +0800 Mime-Version: 1.0 Sent to CCL by: "huanglei" [huanglei-$-mail.utexas.edu] Hi, Jian You may take a look at a program, "gmin" by David J. Wales. http://www-wales.ch.cam.ac.uk/GMIN/ And you have other options: multicanonical sampling, replica exchange sampling, etc. "Tinker" also has some program can work for your purpose. Good luck! -lei ======= 2007-05-18 23:18:06 ======= >Hello, everyone: >I am trying to find the global stable conformation of a complex structure. >Systematic search did not work due to too many rotable bonds. >So I want to try Monte Carlo method. >Can any one tell me how to apply this method and is there any free software >to run? >I will be greatly appreciate your help! > >Jian >