From owner-chemistry@ccl.net Tue Feb 17 03:50:00 2009 From: "Martin Bohl martin%moldiscovery.com" To: CCL Subject: CCL: Release of VolSurf+ software for ADME modelling Message-Id: <-38636-090217030038-31590-klLzgQ8t/R86nwJL4UpC3w/a\server.ccl.net> X-Original-From: "Martin Bohl" Date: Tue, 17 Feb 2009 03:00:34 -0500 Sent to CCL by: "Martin Bohl" [martin{}moldiscovery.com] Dear Colleagues, We would like to draw your attention to the release of VolSurf+ 1.0 for ADME (absorption, distribution, metabolism and excretion) modelling, prediction, and optimisation. The pharmacokinetic behaviour of compounds is linked to their efficacy and thus is critical for drug discovery. Understanding how to optimise compounds according to multiple simultaneous criteria is a great advantage in focusing design efforts. VolSurf+ creates 128 molecular descriptors from 3D Molecular Interaction Fields (MIFs) produced by our software GRID. The new VolSurf+ descriptors significantly outperform previous VolSurf descriptors, have been proven to be particularly relevant to ADME prediction and are also simple to interpret. Examples would be the interaction energy moment descriptor between hydrophobic and hydrophilic regions, which is important for membrane permeability prediction, or the hydrophobic collapse descriptors, which are related to solubility and metabolic stability. These descriptors can then be used with provided chemometric tools to build statistical models. VolSurf+ also comes with a number of models that we have developed using both public and pharmaceutical data, including passive intestinal absorption, blood-brain barrier permeation, solubility, protein binding, volume of distribution, and metabolic stability. VolSurf+ enables users to: - calculate ADME relevant descriptors and perform statistical modelling using experimental data - predict the behaviour of new compounds using custom or established ADME models - interactively sketch structural modifications to optimise ideas according to multiple criteria - select compounds with similar ADME properties to a query structure More information on the original VolSurf method can be found here: J. Mol. Struct. (THEOCHEM) 503, 17-30 (2000). (http://dx.doi.org/10.1016/S0166-1280(99)00360-7). More information about VolSurf+ 1.0 can be found here: http://www.moldiscovery.com/soft_vsplus.php Kind regards, Martin Dr. Martin Bohl Commercial Director Molecular Discovery Ltd Email: martin[at]moldiscovery[dot]com Molecular Discovery provides robust, high-quality and innovative computational methods addressing pharmaceutical needs in the fields of chemoinformatics, ADME and metabolism research. Other Molecular Discovery software products offer calculation of accurate Molecular Interaction Fields for structure-based design (GRID), metabolism prediction (MetaSite), scaffold hopping (SHOP), pKa prediction (MoKa) and general 3D-QSAR modeling (Almond) to improve efficiency in modern drug discovery. More information can be found on the main page: http://www.moldiscovery.com/ From owner-chemistry@ccl.net Tue Feb 17 09:22:00 2009 From: "Hugh Chaffey-Millar hugh.chaffey-millar*|*ch.tum.de" To: CCL Subject: CCL: Gaussian Opti'n for species with very flat methyl rotation potential Message-Id: <-38637-090217074807-14204-3G6L2CnMl2KjM0DLj2Qb8A-*-server.ccl.net> X-Original-From: "Hugh Chaffey-Millar" Date: Tue, 17 Feb 2009 07:48:03 -0500 Sent to CCL by: "Hugh Chaffey-Millar" [hugh.chaffey-millar .. ch.tum.de] Hi I trying to optimise a number of species such as [Mn(NC-CH3)6]2+ and nearly always when attempting to optimise to a minimum, the resulting structure has several imaginary frequencies. I *think* this is because the methyl groups, being so far away from anything else, have a very flat potential well and their individual gradients contribute very little to the set of forces that are analysed by the optimiser. I've attempted using various options to the 'opt' keyword, such as calcall, tight and gdiis but nothing helps. Is there some way of artificially multiplying the gradient associated with these rotations by a factor so that they are given a higher weighting by the optimiser...or something like that? Any suggestions would be much appreciated. Kind regards Hugh From owner-chemistry@ccl.net Tue Feb 17 09:57:00 2009 From: "Yun-an Yan yun-an.yan_._uni-rostock.de" To: CCL Subject: CCL: Spectroscopy corresponding to spectra of velocity autocorrelation Message-Id: <-38638-090217083833-17656-UNCu3teik5eooyGJba7PJg-*-server.ccl.net> X-Original-From: Yun-an Yan Content-Transfer-Encoding: 7BIT Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes Date: Tue, 17 Feb 2009 14:08:42 +0100 MIME-Version: 1.0 Sent to CCL by: Yun-an Yan [yun-an.yan . uni-rostock.de] Dear Colleagues, Would anyone please tell me what is the spectra corresponding to the power spectra of velocity autocorrelation function? Vibration Spectrum or IR or any else? Related references are deeply appreciated. Thank you for your consideration. Best regards, Yun-an Yan From owner-chemistry@ccl.net Tue Feb 17 11:48:00 2009 From: "Maura Mooney mmooney05()qub.ac.uk" To: CCL Subject: CCL: Gromacs installation on Dell Ubuntu Message-Id: <-38639-090217113511-16503-j7gRUgTkyPpJtYUI/M/DWw|-|server.ccl.net> X-Original-From: "Maura Mooney" Date: Tue, 17 Feb 2009 11:35:07 -0500 Sent to CCL by: "Maura Mooney" [mmooney05::qub.ac.uk] Hi all, I am having problem configuring gromacs on my dell machine. I have unzipped the gromacs archive and also the fftw3...tar.gz file (required as a prerequisite). The next step requires cd to the gromacs directory and ./configure. But I can't seem to locate the gromacs directory, or the configure program, thus I cannot go any further with the configuration/installation. The installation appears quite difficult...Can anyone help? :( Thanx, M From owner-chemistry@ccl.net Tue Feb 17 14:22:00 2009 From: "Loan Huynh huynhkl2000]*[yahoo.ca" To: CCL Subject: CCL: Gromacs installation on Dell Ubuntu Message-Id: <-38640-090217132432-15939-FjJ2M1qLJpJfyk9W+9Suhg#,#server.ccl.net> X-Original-From: Loan Huynh Content-Type: multipart/alternative; boundary="0-1093937874-1234891458=:40266" Date: Tue, 17 Feb 2009 09:24:18 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Loan Huynh [huynhkl2000 ~ yahoo.ca] --0-1093937874-1234891458=:40266 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable You should go to Gromacs mailing list.=A0 I'm sure that there are many advi= ce posted already on that list. Here is the link: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ --- On Tue, 2/17/09, Maura Mooney mmooney05()qub.ac.uk wrote: > From: Maura Mooney mmooney05()qub.ac.uk Subject: CCL: Gromacs installation on Dell Ubuntu To: "Huynh, Loan " Received: Tuesday, February 17, 2009, 11:35 AM Sent to CCL by: "Maura Mooney" [mmooney05::qub.ac.uk] Hi all, I am having problem configuring gromacs on my dell machine. I have unzipped= the gromacs archive and also the fftw3...tar.gz file (required as a prerequisit= e). The next step requires cd to the gromacs directory and ./configure. But I can't seem to locate the gromacs directory, or the configure program, thus I cannot go any further with the configuration/installation. The installation appears quite difficult...Can anyone help? :( Thanx, M -=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=0A=0A=0A ____________________________________________________________= ______=0AYahoo! Canada Toolbar: Search from anywhere on the web, and bookma= rk your favourite sites. Download it now at=0Ahttp://ca.toolbar.yahoo.com. --0-1093937874-1234891458=:40266 Content-Type: text/html; charset=us-ascii
You should go to Gromacs mailing list.  I'm sure that there are many advice posted already on that list. Here is the link:
http://www.gromacs.org/component/option,com_wrapper/Itemid,165/

--- On Tue, 2/17/09, Maura Mooney mmooney05()qub.ac.uk <owner-chemistry(~)ccl.net> wrote:
From: Maura Mooney mmooney05()qub.ac.uk <owner-chemistry(~)ccl.net>
Subject: CCL: Gromacs installation on Dell Ubuntu
To: "Huynh, Loan " <huynhkl2000(~)yahoo.ca>
Received: Tuesday, February 17, 2009, 11:35 AM

Sent to CCL by: "Maura  Mooney" [mmooney05::qub.ac.uk]
Hi all,

I am having problem configuring gromacs on my dell machine. I have unzipped the
gromacs archive and also the fftw3...tar.gz file (required as
 a prerequisite).
The next step requires

cd to the gromacs directory and ./configure.

But I can't seem to locate the gromacs directory, or the configure program,
thus I cannot go any further with the configuration/installation.

The installation appears quite difficult...Can anyone help? :(

Thanx,

M





Ask a question on any topic and get answers from real people. Go to Yahoo! Answers. --0-1093937874-1234891458=:40266-- From owner-chemistry@ccl.net Tue Feb 17 14:57:00 2009 From: "Ted Cabeen cabeen]|[chem.ucsb.edu" To: CCL Subject: CCL: Gromacs installation on Dell Ubuntu Message-Id: <-38641-090217143000-22688-qcTRyV9aWdtARmiAirWA+A^^^server.ccl.net> X-Original-From: Ted Cabeen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 17 Feb 2009 10:49:57 -0800 MIME-Version: 1.0 Sent to CCL by: Ted Cabeen [cabeen[]chem.ucsb.edu] You need to untar the file that gunzip created. You should now have a file called fftw3....tar. Run tar xvf fftw3....tar and it will extract what you need. In the future, you can do this in one step by adding the z flag to tar and just running tar xvzf fftw3...tar.gz. --Ted Maura Mooney mmooney05()qub.ac.uk wrote: > Sent to CCL by: "Maura Mooney" [mmooney05::qub.ac.uk] > Hi all, > > I am having problem configuring gromacs on my dell machine. I have unzipped the gromacs archive and also the fftw3...tar.gz file (required as a prerequisite). The next step requires > > cd to the gromacs directory and ./configure. > > But I can't seem to locate the gromacs directory, or the configure program, thus I cannot go any further with the configuration/installation. > > The installation appears quite difficult...Can anyone help? :( > > Thanx, > > M> > From owner-chemistry@ccl.net Tue Feb 17 15:32:00 2009 From: "Roman D Gorbunov rgorbuno() aecom.yu.edu" To: CCL Subject: CCL: Why the Cartesian Force Constants are negative? Message-Id: <-38642-090217143957-27307-hI3/eA85KRQIAavSg8um4Q-$-server.ccl.net> X-Original-From: "Roman D Gorbunov" Date: Tue, 17 Feb 2009 14:39:53 -0500 Sent to CCL by: "Roman D Gorbunov" [rgorbuno*|*aecom.yu.edu] Hi, I think I found out the explanation for the "problem" I had. I just made a wrong assumption about the Hessian matrix (that all elements of this matrix should be positive or zero). By an consideration of a 2 atomic system forming a harmonic oscillator one can easily show that some elements of the Hessian matrix can be negative. Roman From owner-chemistry@ccl.net Tue Feb 17 16:52:01 2009 From: "Xiaohu Li xiaohuli914##gmail.com" To: CCL Subject: CCL: Gromacs installation on Dell Ubuntu Message-Id: <-38643-090217132301-15828-uvQzj3GqZ5FEXaaNlnanjA^^server.ccl.net> X-Original-From: Xiaohu Li Content-Type: multipart/alternative; boundary=0016364270d22e0a7b0463206a3a Date: Tue, 17 Feb 2009 12:12:58 -0500 MIME-Version: 1.0 Sent to CCL by: Xiaohu Li [xiaohuli914__gmail.com] --0016364270d22e0a7b0463206a3a Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Maybe it is better for you to install through the synaptic package manager or through apt which will install the dependencies automatically for you. On Tue, Feb 17, 2009 at 11:35 AM, Maura Mooney mmooney05()qub.ac.uk < owner-chemistry[*]ccl.net> wrote: > > Sent to CCL by: "Maura Mooney" [mmooney05::qub.ac.uk] > Hi all, > > I am having problem configuring gromacs on my dell machine. I have unzipped > the gromacs archive and also the fftw3...tar.gz file (required as a > prerequisite). The next step requires > > cd to the gromacs directory and ./configure. > > But I can't seem to locate the gromacs directory, or the configure program, > thus I cannot go any further with the configuration/installation. > > The installation appears quite difficult...Can anyone help? :( > > Thanx, > > M> > > --0016364270d22e0a7b0463206a3a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Maybe it is better for you to install through the synaptic package manager = or through apt which will install the dependencies automatically for you.
On Tue, Feb 17, 2009 at 11:35 AM, Maura Mo= oney mmooney05()qub.ac.uk <owner-chemistry[*]ccl.net> wrote:

Sent to CCL by: "Maura  Mooney" [mmooney05::qub.ac.uk]
Hi all,

I am having problem configuring gromacs on my dell machine. I have unzipped= the gromacs archive and also the fftw3...tar.gz file (required as a prereq= uisite). The next step requires

cd to the gromacs directory and ./configure.

But I can't seem to locate the gromacs directory, or the configure prog= ram, thus I cannot go any further with the configuration/installation.

The installation appears quite difficult...Can anyone help? :(

Thanx,

M



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--0016364270d22e0a7b0463206a3a-- From owner-chemistry@ccl.net Tue Feb 17 19:13:00 2009 From: "Maura Mooney mmooney05#,#qub.ac.uk" To: CCL Subject: CCL: Gromacs installation on Dell Ubuntu Message-Id: <-38644-090217170341-16254-QQFa5sCvBUKYVunZphKTMA===server.ccl.net> X-Original-From: "Maura Mooney" Date: Tue, 17 Feb 2009 17:03:38 -0500 Sent to CCL by: "Maura Mooney" [mmooney05|*|qub.ac.uk] I have tried this, and it does seem to work but I still cant locate the gromacs directory, which should i think be in /usr/local/gromacs. Any suggestions? Thanx, M > "Ted Cabeen cabeen]|[chem.ucsb.edu" wrote: > > Sent to CCL by: Ted Cabeen [cabeen[]chem.ucsb.edu] > You need to untar the file that gunzip created. You should now have a > file called fftw3....tar. Run tar xvf fftw3....tar and it will extract > what you need. > > In the future, you can do this in one step by adding the z flag to tar > and just running tar xvzf fftw3...tar.gz. > > --Ted > > Maura Mooney mmooney05()qub.ac.uk wrote: > > Sent to CCL by: "Maura Mooney" [mmooney05::qub.ac.uk] > > Hi all, > > > > I am having problem configuring gromacs on my dell machine. I have unzipped the gromacs archive and also the fftw3...tar.gz file (required as a prerequisite). The next step requires > > > > cd to the gromacs directory and ./configure. > > > > But I can't seem to locate the gromacs directory, or the configure program, thus I cannot go any further with the configuration/installation. > > > > The installation appears quite difficult...Can anyone help? :( > > > > Thanx, > > > > M> > > > > From owner-chemistry@ccl.net Tue Feb 17 22:51:00 2009 From: "Gustavo Mercier gamercier---yahoo.com" To: CCL Subject: CCL: Gromacs installation on Dell Ubuntu Message-Id: <-38645-090217212321-15593-YvWiwD45C6nk6neX3ft9LQ^server.ccl.net> X-Original-From: Gustavo Mercier Content-Type: text/plain; charset=us-ascii Date: Tue, 17 Feb 2009 17:23:07 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Gustavo Mercier [gamercier++yahoo.com] Hi! A few recommendations: 1) Get a Linux book that will show a bit about the command line interface, and follow up with one that targets developers. You will learn a lot that you will need to do computational chemistry in linux platforms. 2) Where are the files that you untarred depends: a) Was the tar file created with relative or absolute paths b) How it was untarred, particularly in which directory and if relative or absolute paths were used. I recommend you do the following: 1) Open a terminal for command line entry 2) Execute the following commands in the order listed below: cd $HOME cd tar -ztvf xxx.tar.gz The first command will put you in your default HOME directory. Usually somethin like /home/ The second command moves you to where you placed the xxx.tar.gz files. If you did some download that put the files in a default directory, for example using Firefox, you will have to go to the browser and look where is the default location for downloading files. The last command lists the content of the file and will give you the full name of each member of the archive that makes the file. This name will tell you where the file are located. So if you see something that start like /usr/local/gromacs Then you know you have absolute paths and should look in /usr/local/gromacs if you see gromacs/executable.f Then this is a relative path and you need to look at directory gromacs under the directory that you use to expand the xxx.tar.gz file. Hope this helps! -- Gustavo A. Mercier, Jr. MD,PhD Boston Medical Center Radiology - Nuclear Medicine and Molecular Imaging, Chief gamercier _ yahoo.com (preferred e-mail address) Gustavo.Mercier _ bmc.org gumercie _ bu.edu cell: 469-396-6750 work: 617-638-6610; 617-414-6457 ----- Original Message ---- > From: "Maura Mooney mmooney05#,#qub.ac.uk" To: "Mercier, Gustavo, " Sent: Tuesday, February 17, 2009 5:03:38 PM Subject: CCL: Gromacs installation on Dell Ubuntu Sent to CCL by: "Maura Mooney" [mmooney05|*|qub.ac.uk] I have tried this, and it does seem to work but I still cant locate the gromacs directory, which should i think be in /usr/local/gromacs. Any suggestions? Thanx, M > "Ted Cabeen cabeen]|[chem.ucsb.edu" wrote: > > Sent to CCL by: Ted Cabeen [cabeen[]chem.ucsb.edu] > You need to untar the file that gunzip created. You should now have a > file called fftw3....tar. Run tar xvf fftw3....tar and it will extract > what you need. > > In the future, you can do this in one step by adding the z flag to tar > and just running tar xvzf fftw3...tar.gz. > > --Ted > > Maura Mooney mmooney05()qub.ac.uk wrote: > > Sent to CCL by: "Maura Mooney" [mmooney05::qub.ac.uk] > > Hi all, > > > > I am having problem configuring gromacs on my dell machine. I have unzipped the gromacs archive and also the fftw3...tar.gz file (required as a prerequisite). The next step requires > > > > cd to the gromacs directory and ./configure. > > > > But I can't seem to locate the gromacs directory, or the configure program, thus I cannot go any further with the configuration/installation. > > > > The installation appears quite difficult...Can anyone help? :( > > > > Thanx, > > > > Mhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt