From owner-chemistry@ccl.net Wed Mar 5 04:13:01 2008 From: "soumya samineni soumya_samineni:rediffmail.com" To: CCL Subject: CCL:G: G03:hyperpolarizability Message-Id: <-36418-080305035903-5894-z5416we8AKZrGd2PVZhJXA]*[server.ccl.net> X-Original-From: "soumya samineni" Date: Wed, 5 Mar 2008 03:59:00 -0500 Sent to CCL by: "soumya samineni" [soumya_samineni|*|rediffmail.com] Hi all, 1)I am trying to do a exercise for obtaining hyperpolarizability of molecules. The manual says: In the gaussian calculation, it writes 6- components for the alpha(xx),alpha(yy) alpha(zz) alpha(xy) alpha(yz) alpha (zx) Is it that i need to do the RMS of the 6-components to get the final first order HYPERPOLARIZABILTY of the molecule. 2)Where can i find experimentally reported Hyperpolarizabilty values thanx in advance soumya From owner-chemistry@ccl.net Wed Mar 5 05:23:00 2008 From: "Jamie Platts platts**Cardiff.ac.uk" To: CCL Subject: CCL: MGMS Spring Meeting Message-Id: <-36419-080305044312-22858-SrDyitp2sii3Q6yep9sacA,server.ccl.net> X-Original-From: "Jamie Platts" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Wed, 05 Mar 2008 09:42:49 +0000 Mime-Version: 1.0 Sent to CCL by: "Jamie Platts" [platts|,|Cardiff.ac.uk] Dear Colleague A full programme for the MGMS Spring 2008 meeting is now available at http://theory.chem.cf.ac.uk/~grant/conf/prog.html Registration for the meeting is still open. As you will see from the link above, we have an excellent and varied list of speakers. The meeting will include the AGM of the Molecular Graphics and Modelling Society as part of the afternooon session of Monday 31st March. Jamie Platts ---------------------------------------------------------- Jamie Platts School of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts:_:cf.ac.uk Park Place FAX: +44 (0) 2920 874030 Cardiff CF10 3AT www.cf.ac.uk/chemy From owner-chemistry@ccl.net Wed Mar 5 05:52:01 2008 From: "Andrew Turner andrew.turner*ed.ac.uk" To: CCL Subject: CCL:G: Simple Batch/Queue Software for Linux 64-bit/ Gaussian 03 Message-Id: <-36420-080305043937-21050-j8kt1egSn+HN11jh5UgsEw!A!server.ccl.net> X-Original-From: Andrew Turner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 05 Mar 2008 09:00:34 +0000 MIME-Version: 1.0 Sent to CCL by: Andrew Turner [andrew.turner.:.ed.ac.uk] We use Sun Grid Engine. Easy to set up and use. http://gridengine.sunsource.net/ Andy Soren Eustis soren###jhu.edu wrote: > Sent to CCL by: "Soren Eustis" [soren- -jhu.edu] > I have relied on WebMo to handle my queuing for G03 on windows. Now that I have G03 running on my Linux EM64T, I would love to get that working as well. However, for the time being it has eluded me. > > In the mean time, can anyone recommend a simple batch program that will work under Linux (OpenSuse to be specific). The Gaussian manual talks about NQS... > > Thanks in advance. > > Soren Eustis > Department of Chemistry > Johns Hopkins University> > > -- ================================== Dr Andrew R. Turner Research Computing Officer e: andrew.turner!^!ed.ac.uk t: +44 (0)131 650 7748 w: http://www.eastchem.ac.uk/rcf icq: 370-899-715 p: School of Chemistry University of Edinburgh EH9 3JJ ================================== From owner-chemistry@ccl.net Wed Mar 5 06:27:00 2008 From: "Justin Finnerty justin.finnerty]=[uni-oldenburg.de" To: CCL Subject: CCL:G: Simple Batch/Queue Software for Linux 64-bit/ Gaussian 03 Message-Id: <-36421-080305060153-32685-nR6ysY7kKZ8RBh7hudaVzw|,|server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 05 Mar 2008 10:11:41 +0100 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty ~~ uni-oldenburg.de] On Tue, 2008-03-04 at 14:41 -0500, Soren Eustis soren###jhu.edu wrote: > Sent to CCL by: "Soren Eustis" [soren- -jhu.edu] > In the mean time, can anyone recommend a simple batch program that will work under Linux > (OpenSuse to be specific). The Gaussian manual talks about NQS... If you are talking about a single machine with few/single user then the "batch" and "at" commands are the way to go. I think these are part of the basic Suse install, otherwise install the "at" package. You may need to check that the "at" daemon (called atd) is running, it is off be default (use "chkconfig -c atd", "chkconfig -a atd" to add or use Yast2/System Services). This queue is load based FIFO queue - when the machine has no load it starts the next submitted job. A much more flexible, though complex, choice is torque (optionally with maui) from www.clusterresources.com. This is an implementation of the POSIX PBS queue system, of which the mentioned NQS is another example. These are opensource projects that will require compilation on your system but they are needed if you have multiple machines. The SunGridEngine is also another free or opensource project for queue systems on multiple machines. Cheers Justin -- Dr Justin Finnerty Rm W3-1-165 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Wed Mar 5 07:02:01 2008 From: "Tanja van Mourik tanja.vanmourik|,|st-andrews.ac.uk" To: CCL Subject: CCL: Coupled Cluster and MP4 in peptides Message-Id: <-36422-080305054518-21020-DoaHEffzPwSKE6uS41m7qA*server.ccl.net> X-Original-From: Tanja van Mourik Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 5 Mar 2008 10:13:13 +0000 MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [tanja.vanmourik|,|st-andrews.ac.uk] Hi Pablo, > In my group, at the University of Zaragoza, we are planning to build a new > cluster to perform high-level QC calculations. Meaning CCSD, CCSD(T), > MP4(SDQ) and MP4, with basis sets (Dunning's, for example) of, say, double-, > triple- and quadruple-zeta quality (if possible). > > To begin with, we are interested in capped peptide systems with 1 or 2 > residues. Being Tryptophan the largest natural residue, the largest peptide > we need to deal with is probably the 2-Tryptophan. A 1-Tryptophan has 17 > 1st-row atoms and 12 hydrogens, while a 2-Tryptophan has 31 1st-row atoms > and 21 hydrogens (assuming formyl and amide cappings). Just a note on the level of theory required for such calculations: Because of likely pi interactions in peptides with aromatic rings, both dispersion and intramolecular BSSE are expected to be large. Even with basis sets like aug-cc-pVDZ and aug-cc-pVTZ the BSSE may be still large enough to distort the potential energy surface, see Chem Phys. Lett. 442, 42-46 (2007) and J. Phys. Chem. A 111, 13272-13277 (2007). Have you considered using local methods (LMP2, LCCSD(T)), which reduce the magnitude of the BSSE, or perhaps density functionals developed for weak interactions? Calculations on this level of theory will be very demanding in CPU, memory and disk. On our cluster, we have 2GB memory per core and frequently cannot do such calculations because we would need more (this is for df-LCCSD(T0), which is less demanding than canonical CCSD(T)). If you are looking for a cluster, you also need local disks on the compute nodes. Best wishes, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow School of Chemistry, University of St. Andrews North Haugh, St. Andrews Fife KY16 9ST, Scotland (UK) email: tanja.vanmourik%%st-andrews.ac.uk web: http://chemistry.st-and.ac.uk/staffmember.php?id=tvm ================================================================= > > We would like to calculate single-point energies, gradients and maybe second > derivatives of the energy of these systems using the aforementioned levels > of the quantum chemical theory. > > We would thank any data regarding the hardware requirements to perform these > calculations, meaning minimum RAM memory, disk space and 1-node > CPU/wall-clock time. As well as the relation of these requirements with the > different existing codes. > > This will help us choose the best architecture for the new cluster. > > Thank you very much in advance. > > -- > Pablo Echenique > > Instituto de Biocomputación y > Física de los Sistemas Complejos (BIFI) > > Departamento de Física Teórica > Universidad de Zaragoza > Pedro Cerbuna 12, 50009 Zaragoza > Spain > > Tel.: +34 976761260 > Fax: +34 976761264 > > echenique.p-x-gmail.com > http://www.pabloechenique.com > ------------------------------------------------------------------ University of St Andrews Webmail: https://webmail.st-andrews.ac.uk From owner-chemistry@ccl.net Wed Mar 5 07:54:00 2008 From: "teorica.ch*_*unito.it" To: CCL Subject: CCL:G: need a program for vibration analysis Message-Id: <-36423-080305063614-32056-FODmIU5Hak10QmcKSfHBig~~server.ccl.net> X-Original-From: teorica.ch(!)unito.it Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 5 Mar 2008 11:56:03 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: teorica.ch ~ unito.it See vibrational analysis performed by CRYSTAL06 program http://www.crystal.unito.it/vibrations Full output at the bottom of the file. Carla Roetti Theoretical Chemistry Group - Torino > > > ------------------ Messaggio originale ------------------- > Oggetto: CCL:G: need a program for vibration analysis > Da: "Philippe Carbonniere philippe.carbonniere .. > univ-pau.fr" > Data: Mar, 4 Marzo 2008, 9:03 am > A: "Roetti, Carla " > ---------------------------------------------------------- > > > Sent to CCL by: Philippe Carbonniere > [philippe.carbonniere*|*univ-pau.fr] > Hi ! > > What do you mean by "vibrational analysis3 ? > If you wish to visualize gaussian vibrational data, you > can use Molden > for instance. > > Hope this helps, > > Philippe Carbonniere > > > Quoting "Guanna Li gnli#dicp.ac.cn" > : > >> >> Sent to CCL by: "Guanna Li" [gnli%%dicp.ac.cn] >> Dear all, >> I use Gaussian to do frequency calculation, >> and i want to >> find a program which can do vibration analysis, anybody >> who knows >> please help me! Thank you ! >> >> -------------- >> 2008-03-03 >> Best wishes >> >> Guanna Li >> Email: gnli a dicp.ac.cn >> >> >> >> -= This is automatically added to each message by the >> mailing script =-> >> >> > > > > -To recover the email address of the author of the > message, please change > the strange characters on the top line to the :-: sign. You > can also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > > > From owner-chemistry@ccl.net Wed Mar 5 08:35:01 2008 From: "Igor Filippov Contr igorf_-_helix.nih.gov" To: CCL Subject: CCL: Structure of few compounds Message-Id: <-36424-080305001151-1873-UT+rANO3hvbIGNZemoF31g%%server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 04 Mar 2008 22:46:35 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf#%#helix.nih.gov] Not exactly what you're looking for, but for what it's worth... Hexalgon hydrobromide http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=22390 Triprolidine.HCl monohydrate http://potency.berkeley.edu/chempages/TRIPROLIDINE.HCl% 20MONOHYDRATE.html and a few other names containing "prolidine" http://www.emolecules.com/cgi-bin/search?t=ss&v=&c=&q=prolidine Cheers, Igor On Tue, 2008-03-04 at 06:26 -0500, Sherin Falah shireen.alfalah*yahoo.com wrote: > > Sent to CCL by: "Sherin Falah" [shireen.alfalah(~)yahoo.com] > Dear CCL users, > I am looking for the structure of some compounds but I can not find > them. I would be very grateful if someone can provide me with the > chemical structure for these compounds. > > The compounds are: > 1. Aminochlorothenoxazin > 2. dipanone > 3. prolidine > 4. hexalgon > > Thanks in advance. > > Best regards, > Shireen Falah > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -- Igor Filippov [Contr] From owner-chemistry@ccl.net Wed Mar 5 09:42:00 2008 From: "Martin Bohl martin/./moldiscovery.com" To: CCL Subject: CCL: pKa prediction and tautomer modelling software MoKa Message-Id: <-36425-080305040435-6419-rTEd6iMaa+auc+9fsk6PFw^^^server.ccl.net> X-Original-From: "Martin Bohl" Date: Wed, 5 Mar 2008 04:04:30 -0500 Sent to CCL by: "Martin Bohl" [martin#moldiscovery.com] New Release: Announcing the launch of MoKa 1.0 software for pKa and tautomer modelling Dear Colleagues, We would like to draw your attention to Moka 1.0 software for the pKa prediction of organic compounds. Accurate pKa prediction and automatic structure modification is critical for many computational chemistry methods. Docking and binding affinity prediction using the incorrectly ionized structure (or at the very least the same ionization state as the docking software was parameterized with) will severely negate the usefulness of the results. Key parameters such as solubility and lipophilicity are governed by pKa. If a structure can exist with a small amount of the neutral species at a given pH, ADME prediction (eg. membrane permeation) can also be significantly affected. MoKa implements a novel approach using GRID based Molecular Interaction Fields (MIFs) as descriptors, which were then used to develop, train, and cross-validate a large number of models covering various chemical functionality, using 25,000 pKa values. More detail is available in the publication: J. Chem. Inf. Model., 47(6), 2172-2182 (2007) (http://dx.doi.org/10.1021/ci700018y). Key features of Moka include: - Accuracy: prediction error of 0.4 log units (0.7 for novel structures) - Speed: more than 1 million predictions per hour - Automation: output the top N species at a designated pH - Self-trainable: incorporate your own experimental data to further improve accuracy Moka comes with an easy-to-use graphical interface for pKa assignment, enabling you to graphically profile the species abundance. Incorrect or unlikely tautomers are automatically flagged for your attention. Predictions for large numbers of compounds can be easily compared with experimental data or other methods. Command-line tools are also provided, enabling users to output (a) the single most abundant species at a given pH, (b) multiple states across a pH range, (c) enumerated tautomers, or (d) estimation of tautomer stability. Moka is available on Windows and Linux platforms. More information about MoKa can be found here: www.moldiscovery.com/soft_moka.php More information about other Molecular Discovery products (GRID, Almond, VolSurf, MetaSite, SHOP) can be found on the main page: www.moldiscovery.com As with all of our software, it is available in single user and site licenses, and affordable academic versions are available. Two-week evaluations are also available for commercial users. Please contact sales_at_moldiscovery_dot_com if you would like to know more. Kind Regards, Martin Dr Martin Bohl Commercial Director Molecular Discovery Ltd From owner-chemistry@ccl.net Wed Mar 5 13:19:01 2008 From: "Pablo Echenique echenique.p]^[gmail.com" To: CCL Subject: CCL: Coupled Cluster and MP4 in peptides Message-Id: <-36426-080305130823-4411-Y43T7QKpP4tzckOQKIuedQ=-=server.ccl.net> X-Original-From: "Pablo Echenique" Content-Type: multipart/alternative; boundary="----=_Part_8489_2033966.1204740459289" Date: Wed, 5 Mar 2008 19:07:39 +0100 MIME-Version: 1.0 Sent to CCL by: "Pablo Echenique" [echenique.p ~~ gmail.com] ------=_Part_8489_2033966.1204740459289 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Tanja, On Wed, Mar 5, 2008 at 11:13 AM, Tanja van Mourik tanja.vanmourik|,|st- andrews.ac.uk wrote: > > Sent to CCL by: Tanja van Mourik [tanja.vanmourik|,|st-andrews.ac.uk] > Hi Pablo, > > > In my group, at the University of Zaragoza, we are planning to build a > new > > cluster to perform high-level QC calculations. Meaning CCSD, CCSD(T), > > MP4(SDQ) and MP4, with basis sets (Dunning's, for example) of, say, > double-, > > triple- and quadruple-zeta quality (if possible). > > > > To begin with, we are interested in capped peptide systems with 1 or 2 > > residues. Being Tryptophan the largest natural residue, the largest > peptide > > we need to deal with is probably the 2-Tryptophan. A 1-Tryptophan has 1= 7 > > 1st-row atoms and 12 hydrogens, while a 2-Tryptophan has 31 1st-row > atoms > > and 21 hydrogens (assuming formyl and amide cappings). > > Just a note on the level of theory required for such calculations: Becaus= e > of > likely pi interactions in peptides with aromatic rings, both dispersion > and > intramolecular BSSE are expected to be large. Even with basis sets like > aug-cc-pVDZ and aug-cc-pVTZ the BSSE may be still large enough to distort > the > potential energy surface, see Chem Phys. Lett. 442, 42-46 (2007) and J. > Phys. > Chem. A 111, 13272-13277 (2007). Have you considered using local methods > (LMP2, > LCCSD(T)), which reduce the magnitude of the BSSE, or perhaps density > functionals developed for weak interactions? > No, that's a very good point. There are so many methods to try that we will have to go probably for a flexible architecture that allows all of them to be run with moderate efficiency. > > Calculations on this level of theory will be very demanding in CPU, memor= y > and > disk. On our cluster, we have 2GB memory per core and frequently cannot d= o > such > calculations because we would need more (this is for df-LCCSD(T0), which > is less > demanding than canonical CCSD(T)). If you are looking for a cluster, you > also > need local disks on the compute nodes. > Ok, do you have some estimation of how much RAM and disk would it take to run CCSD(T) single-points and/or optimizations in a 2-Tryptophan? Best wishes, Pablo. > > Best wishes, > > Tanja > -- > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > Tanja van Mourik > Royal Society University Research Fellow > School of Chemistry, University of St. Andrews > North Haugh, St. Andrews > Fife KY16 9ST, Scotland (UK) > > email: tanja.vanmourik[a]st-andrews.ac.uk > web: http://chemistry.st-and.ac.uk/staffmember.php?id=3Dtvm > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > > > We would like to calculate single-point energies, gradients and maybe > second > > derivatives of the energy of these systems using the aforementioned > levels > > of the quantum chemical theory. > > > > We would thank any data regarding the hardware requirements to perform > these > > calculations, meaning minimum RAM memory, disk space and 1-node > > CPU/wall-clock time. As well as the relation of these requirements with > the > > different existing codes. > > > > This will help us choose the best architecture for the new cluster. > > > > Thank you very much in advance. > > > > -- > > Pablo Echenique > > > > Instituto de Biocomputaci=F3n y > > F=EDsica de los Sistemas Complejos (BIFI) > > > > Departamento de F=EDsica Te=F3rica > > Universidad de Zaragoza > > Pedro Cerbuna 12, 50009 Zaragoza > > Spain > > > > Tel.: +34 976761260 > > Fax: +34 976761264 > > > > echenique.p-x-gmail.com > > http://www.pabloechenique.com > > > > > > > ------------------------------------------------------------------ > University of St Andrews Webmail: https://webmail.st-andrews.ac.uk > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Pablo Echenique Instituto de Biocomputaci=F3n y F=EDsica de los Sistemas Complejos (BIFI) Departamento de F=EDsica Te=F3rica Universidad de Zaragoza Pedro Cerbuna 12, 50009 Zaragoza Spain Tel.: +34 976761260 Fax: +34 976761264 echenique.p*gmail.com http://www.pabloechenique.com ------=_Part_8489_2033966.1204740459289 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Tanja,

On Wed, Mar 5, 2008 at 11:13 AM= , Tanja van Mourik tanja.vanmourik|,|st-an= drews.ac.uk <owner-chemis= try*ccl.net> wrote:

Sent to CCL by: Tanja van Mourik [tanja.vanmourik|,|st-andrews.ac.uk]
Hi Pablo,

> In my group, at the University of Zaragoza, we are planning to build a= new
> cluster to perform high-level QC calculations. Meaning CCSD, CCSD(T),<= br> > MP4(SDQ) and MP4, with basis sets (Dunning's, for example) of, say= , double-,
> triple- and quadruple-zeta quality (if possible).
>
> To begin with, we are interested in capped peptide systems with 1 or 2=
> residues. Being Tryptophan the largest natural residue, the largest pe= ptide
> we need to deal with is probably the 2-Tryptophan. A 1-Tryptophan has = 17
> 1st-row atoms and 12 hydrogens, while a 2-Tryptophan has 31 1st-row at= oms
> and 21 hydrogens (assuming formyl and amide cappings).

Just a note on the level of theory required for such calculations: Because = of
likely pi interactions in peptides with aromatic rings, both dispersion and=
intramolecular BSSE are expected to be large. Even with basis sets like
aug-cc-pVDZ and aug-cc-pVTZ the BSSE may be still large enough to distort t= he
potential energy surface, see Chem Phys. Lett. 442, 42-46 (2007) and J. Phy= s.
Chem. A 111, 13272-13277 (2007). Have you considered using local methods (L= MP2,
LCCSD(T)), which reduce the magnitude of the BSSE, or perhaps density
functionals developed for weak interactions?

No, that's a very good point. There are so many m= ethods to try that we will have to go probably for a flexible architecture = that allows all of them to be run with moderate efficiency.

Calculations on this level of theory will be very demanding in CPU, memory = and
disk. On our cluster, we have 2GB memory per core and frequently cannot do = such
calculations because we would need more (this is for df-LCCSD(T0), which is= less
demanding than canonical CCSD(T)). If you are looking for a cluster, you al= so
need local disks on the compute nodes.

Ok, do you have some estimation of how much RAM and d= isk would it take to run CCSD(T) single-points and/or optimizations in a 2-= Tryptophan?

Best wishes,

  Pablo.

Best wishes,

Tanja
--
 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
  Tanja van Mourik
  Royal Society University Research Fellow
  School of Chemistry, University of St. Andrews
  North Haugh, St. Andrews
  Fife KY16 9ST, Scotland (UK)

  email: tanja.vanmourik[a]st-andrews.ac.uk
  web:   http://chemistry.st-and.ac.uk/staffmember.php= ?id=3Dtvm
  =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>
> We would like to calculate single-point energies, gradients and maybe = second
> derivatives of the energy of these systems using the aforementioned le= vels
> of the quantum chemical theory.
>
> We would thank any data regarding the hardware requirements to perform= these
> calculations, meaning minimum RAM memory, disk space and 1-node
> CPU/wall-clock time. As well as the relation of these requirements wit= h the
> different existing codes.
>
> This will help us choose the best architecture for the new cluster. >
> Thank you very much in advance.
>
> --
> Pablo Echenique
>
> Instituto de Biocomputaci=F3n y
> F=EDsica de los Sistemas Complejos (BIFI)
>
> Departamento de F=EDsica Te=F3rica
> Universidad de Zaragoza
> Pedro Cerbuna 12, 50009 Zaragoza
> Spain
>
> Tel.:   +34 976761260
> Fax:    +34 976761264
>
> echenique= .p-x-gmail.com
> http://www= .pabloechenique.com
>




------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY*ccl.n= et or use:
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEM= ISTRY-REQUEST*ccl.net or use
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
     http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: htt= p://www.ccl.net/htdig  (login: ccl, Password: search)
     http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
Pablo Echenique

= Instituto de Biocomputaci=F3n y
F=EDsica de los Sistemas Complejos (BIFI= )

Departamento de F=EDsica Te=F3rica
Universidad de Zaragoza
P= edro Cerbuna 12, 50009 Zaragoza
Spain

Tel.:   +34 976761260
Fax:    +34 976761264<= br>
echenique.p*gmail.comhttp://www.pabloechenique.com ------=_Part_8489_2033966.1204740459289-- From owner-chemistry@ccl.net Wed Mar 5 13:53:01 2008 From: "Jerome Kieffer jerome.Kieffer]-[terre-adelie.org" To: CCL Subject: CCL:G: Simple Batch/Queue Software for Linux 64-bit/ Gaussian 03 Message-Id: <-36427-080305130830-4442-QptQ5L36p/GdBmb65zYScw{=}server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Wed, 5 Mar 2008 19:08:06 +0100 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer(a)terre-adelie.org] On Tue, 4 Mar 2008 14:41:04 -0500 "Soren Eustis soren###jhu.edu" wrote: >=20 > Sent to CCL by: "Soren Eustis" [soren- -jhu.edu] > I have relied on WebMo to handle my queuing for G03 on windows. Now that= I have G03 running on my Linux EM64T, I would love to get that working as = well. However, for the time being it has eluded me. =20 >=20 > In the mean time, can anyone recommend a simple batch program that will w= ork under Linux (OpenSuse to be specific). The Gaussian manual talks about= NQS... I use Torque/OpenPBS : it works well and it is free + open-source. Regards. --=20 J=E9r=F4me KIEFFER : http://www.terre-adelie.org From owner-chemistry@ccl.net Wed Mar 5 22:29:00 2008 From: "Fan,Huajun hjfan\a/pvamu.edu" To: CCL Subject: CCL: ADME predict software Message-Id: <-36428-080305220957-7206-0UrvqLVww0Je50yNyrV84Q^server.ccl.net> X-Original-From: "Fan,Huajun" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C87F32.125F9A99" Date: Wed, 5 Mar 2008 20:30:34 -0600 MIME-Version: 1.0 Sent to CCL by: "Fan,Huajun" [hjfan-*-pvamu.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C87F32.125F9A99 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all: Could anyone tell me where I can find ADME prediction sofwre for a = database or lists compouds in sdf format? I remember seeing such post = here but I couldn't find in my email or ccl websit. Also, does anyone = know if ADME database or libaray or something like that exists. Thanks! Huajun ------_=_NextPart_001_01C87F32.125F9A99 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =0A= =0A= =0A= Hi all:
Could anyone tell me where I can find ADME prediction = sofwre for a database or lists compouds in sdf format? I = remember seeing such post here but I couldn't find in my email or ccl = websit. Also, does anyone know if ADME database or libaray or something = like that exists.
Thanks! Huajun ------_=_NextPart_001_01C87F32.125F9A99-- From owner-chemistry@ccl.net Wed Mar 5 23:13:00 2008 From: "aarsiv aardak compchem2008{=}gmail.com" To: CCL Subject: CCL: Protein-RNA docking program Message-Id: <-36429-080304105830-29941-kUVK9JsSt7gUrbvj1Qs8pg : server.ccl.net> X-Original-From: "aarsiv aardak" Content-Type: multipart/alternative; boundary="----=_Part_23142_12837499.1204646298973" Date: Tue, 4 Mar 2008 10:58:18 -0500 MIME-Version: 1.0 Sent to CCL by: "aarsiv aardak" [compchem2008]![gmail.com] ------=_Part_23142_12837499.1204646298973 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi CCLers, Would anybody provide me the online web server program to predict Protein-RNA interaction complex. Thanks in advance, Daky ------=_Part_23142_12837499.1204646298973 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi CCLers,
Would anybody provide me the online web server program to predict Protein-RNA interaction complex.
 
Thanks in advance,
Daky  ------=_Part_23142_12837499.1204646298973--