From owner-chemistry@ccl.net Tue Dec 16 00:16:00 2008 From: "Antonio G. De Crisci antonio.decrisci ~ utoronto.ca" To: CCL Subject: CCL: Millsian 1.0 Message-Id: <-38304-081216001435-4970-omSi0bxvV1gwA9leqYnpKA_-_server.ccl.net> X-Original-From: "Antonio G. De Crisci" Date: Tue, 16 Dec 2008 00:14:32 -0500 Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci-.-utoronto.ca] Hello All, Has anybody used this program found at the link below? http://www.millsian.com/ Its still in development, but I like the idea of not using super computer for large system. It doesnt use the laws of QM, but yet is able to predict properties of organic molecules quite accurately using classical physics? Anthony From owner-chemistry@ccl.net Tue Dec 16 00:56:01 2008 From: "hirdesh kumar hirdeshs8],[gmail.com" To: CCL Subject: CCL: How to run jobs in background for linux based schrodinger system Message-Id: <-38305-081215061631-14435-Jjp+vdZD8Lprytk4hMVE0w(_)server.ccl.net> X-Original-From: "hirdesh kumar" Content-Type: multipart/alternative; boundary="----=_Part_148356_3570942.1229337810303" Date: Mon, 15 Dec 2008 16:13:30 +0530 MIME-Version: 1.0 Sent to CCL by: "hirdesh kumar" [hirdeshs8---gmail.com] ------=_Part_148356_3570942.1229337810303 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline To all; I am using linux based schrodinger software and i want to use glide as well as induce fit docking module at a time. Can any one please tell me how can i run more than one jobs in background.? -- Hirdesh Kumar Sharma M.S. 3rd Sem. Center for Pharmacoinformatics NIPER, Sector 67, S.A.S. Nagar, Mohali Punjab-160062 ------=_Part_148356_3570942.1229337810303 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline To all;
I am using linux based schrodinger software and i want to use glide as well as induce fit docking module at a time. Can any one please tell me how can i run more than one jobs in background.?


--
Hirdesh Kumar Sharma
M.S. 3rd Sem.
Center for Pharmacoinformatics
NIPER,
Sector 67, S.A.S. Nagar, Mohali
Punjab-160062
------=_Part_148356_3570942.1229337810303-- From owner-chemistry@ccl.net Tue Dec 16 01:31:01 2008 From: "Aditya Chhikara adichhikara(-)gmail.com" To: CCL Subject: CCL: problem generating cube files- Total density not found on fchk file Message-Id: <-38306-081216004546-18419-UI6tqm9BNCzcdESD3ZqyzQ+/-server.ccl.net> X-Original-From: "Aditya Chhikara" Date: Tue, 16 Dec 2008 00:45:41 -0500 Sent to CCL by: "Aditya Chhikara" [adichhikara^_^gmail.com] Hello, I'm trying to generate a .cube file from a .fchk file but am getting the error "Total density not found on fchk file" I successfully generated the .fchk file from the .chk file using the formchk keyword. For generating the .chk file, I used the pop=full keyword. My command line is: cubegen 0 density=scf filename.fchk filename.cube 0 h If anybody has had this problem before, and knows to solve it, please advise. Thanks, Adi Chhikara From owner-chemistry@ccl.net Tue Dec 16 02:47:01 2008 From: "Daniil Bratashov dn2010,,gmail.com" To: CCL Subject: CCL: share information adbout your favorite soft and web tutorials Message-Id: <-38307-081216024057-26471-h3+8LACW4f12LiGw3m5arA---server.ccl.net> X-Original-From: Daniil Bratashov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Tue, 16 Dec 2008 10:40:30 +0300 Mime-Version: 1.0 Sent to CCL by: Daniil Bratashov [dn2010_+_gmail.com] On Mon, 15 Dec 2008 17:38:28 -0500 "Anatoli Korkin a_korkin\a/yahoo.com" wrote: > Sent to CCL by: "Anatoli Korkin" [a_korkin*yahoo.com] > We are planning to update the links at the "software" and "education > pages at ASDN: > > http://www.asdn.net/asdn/links/software.shtml In Design & Visualization: ghemical http://www.uku.fi/~thassine/projects/ghemical/ wxmacmolplt http://www.scl.ameslab.gov/MacMolPlt/ In Classical Mechanics & Molecular Dynamics: AMBER is commercial software (Fees: Academic/non-profit/government: $400. Industrial (for-profit): $20,000 for new licensees, $15,000 for licensees of Amber 9. Porting and demonstration licenses are available; see the License Agreement for details.) In Quantum Mechanics: PC GAMESS/Firefly http://classic.chem.msu.su/gran/gamess/index.html WBR, Daniil Bratashov. From owner-chemistry@ccl.net Tue Dec 16 03:33:01 2008 From: "kshatresh kshatresh+*+gmail.com" To: CCL Subject: CCL: How to run jobs in background for linux based schrodinger system Message-Id: <-38308-081216032628-29537-uafE97op/TVUn4U1s3BiuA++server.ccl.net> X-Original-From: kshatresh Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; delsp=yes; charset=utf-8 Date: Sat, 20 Sep 2008 12:17:22 -0700 MIME-Version: 1.0 Sent to CCL by: kshatresh [kshatresh|gmail.com] Hi Hirdesh .. if your system have more than one processer than surely you can run more than one jobs simulataeneously. It's very simple...go to maestro module...open application...then run glide as you want ...now you can close that application ,it will run in background untill job incorporation...same time u can go in workflow and run induced fit docking as u want.. For further assistance u are always welcome... Kshatresh Dutta Dubey Research Scholar (Computational Molecular Biophysics) > To all; > I am using linux based schrodinger software and i want to use glide as > well > as induce fit docking module at a time. Can any one please tell me how > can i > run more than one jobs in background.? > > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From owner-chemistry@ccl.net Tue Dec 16 12:20:01 2008 From: "Richard Henchman henchman~!~manchester.ac.uk" To: CCL Subject: CCL: translational entropy and solvation Message-Id: <-38309-081216085341-1727-QmQDXrXaqrJcdlE9K+OPLw=server.ccl.net> X-Original-From: "Richard Henchman" Date: Tue, 16 Dec 2008 08:53:37 -0500 Sent to CCL by: "Richard Henchman" [henchman,manchester.ac.uk] It is possible to regard a solute as having the ideal-gas entropy in solution, but it is not the only possibility because there is no unique way to allocate entropy to each molecule in the solution, as Raphael Ribeiro (9 Dec) and Mike Gilson (11 Dec) have already pointed out. This can be made clear by considering the example of water dissolved in water (use D2O if you prefer to have labels and ignoring the fact that it would form HOD). If you assign this solute water the ideal-gas entropy (~129 J/K/mol at 298 K for water at the density of liquid water), then the entropy of the surrounding water molecules is reduced due to excluded volume by the solute, as is the common practice. This ensures that the total entropy of the solution equals that of bulk water. Another possibility is to give the solute water molecule the same entropy of all the other water molecules i.e. less than the gas phase (~70 J/K/mol at 298 K). How one could calculate such an entropy I have shown in some recent publications on water: http://link.aip.org/link/?JCP/126/064504 and a quantised version http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/2008/112/i32/abs/jp0737303.html These same ideas would apply to any solute, not just a solute water molecule. The solute would have lower entropy than the ideas-gas value due to confinement by the solvent. The solute takes all possible positions and orientations but its freedom is still constrained by where the other solvent molecules are. If this seems counter-intuitive, it is only because the dimensionality of 3N-space is so large. One could even consider a case intermediate between the confined solute and the ideal-gas solute. In any case, whichever solution model one uses, the solute and solvent entropy must add up to give the total entropy of the solution. I think a number of contributors to this discussion are right to question whether current solvation models do this. A few other comments: Andreas Klamt is correct to emphasise that the ideal-gas entropy should be 3k/2 and not 5k/2 because the entropy relates to a single molecule. However, I am not convinced by the statement that "the solvent definitely reduces the motional (kinetic) phase space". That amounts to saying that the solvent is at a lower temperature. Ignoring quantum effects, which I believe to be small (based on my second publication given above), the momentum partition functions should be very similar. Richard Henchman __ Dr Richard H Henchman The University of Manchester http://personalpages.manchester.ac.uk/staff/henchman/ From owner-chemistry@ccl.net Tue Dec 16 12:59:00 2008 From: "Emilio =?ISO-8859-1?Q?Jos=E9_Ju=E1rez_P=E9rez?= ejjuarez|*|icmab.es" To: CCL Subject: CCL: Nitroethane crystal structure Message-Id: <-38310-081216123126-29205-aMOuE/hDbfYqLlMe5JkzbA^server.ccl.net> X-Original-From: Emilio =?ISO-8859-1?Q?Jos=E9_Ju=E1rez_P=E9rez?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Tue, 16 Dec 2008 16:32:38 +0100 Mime-Version: 1.0 Sent to CCL by: Emilio =?ISO-8859-1?Q?Jos=E9_Ju=E1rez_P=E9rez?= [ejjuarez:-:icmab.es] Hello, Maybe I dont understand very well the question but the crystal structures in the Cambridge Structural Database with refcodes : DAKROW, DITGUI, DOJZOR, PIKHUM, QALNUK, TAXKUY, ZZZUXO and ZZZUXY contains nitroethane as estructural solvent. El lun, 15-12-2008 a las 18:49 -0500, Oscar U Ojeda oscar.ojeda{=}chemail.tamu.edu escribió: > Sent to CCL by: "Oscar U Ojeda" [oscar.ojeda~~chemail.tamu.edu] > Dear CCL peers; > For some reason, the crystal structure of this solvent (EtNO2) seems to escape from traditional (ISI, CCSD, etc.) resource hits. I would appreciate any pointers. > Cheers > Oscar> ________________________________________________________________________ Emilio José Juárez-Pérez PhD Student ICMAB-CSIC Campus UAB 08193 Bellaterra (Barcelona) Spain. ejjuarez::icmab.es http://www.emiliojuarez.es Tel. + 34 93 580 1853 (ext. 255) Fax + 34 93 580 5729 ________________________________________________________________________ From owner-chemistry@ccl.net Tue Dec 16 14:07:00 2008 From: "Nicholas Labello label030++umn.edu" To: CCL Subject: CCL: Millsian 1.0 Message-Id: <-38311-081216133450-4406-/1DyB9xGAi07deKEs3jwxg() server.ccl.net> X-Original-From: Nicholas Labello Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 16 Dec 2008 12:05:09 -0600 MIME-Version: 1.0 Sent to CCL by: Nicholas Labello [label030[#]umn.edu] The theories that drive that program are not accepted by the greater scientific community (or any scientific community that I am aware of). The company (Black Light Power and/or Millsian, Inc.) posted a job offer on the CCL list a few months ago and I looked into it a bit. After some reading I became convinced that the program you asked about and parent companies are in the absolute best light founded on misguided scientific principles and at worst are simply fraudulent. Stay away from it. Please see the "controversy" section in the following wiki: http://en.wikipedia.org/wiki/Hydrino Nick Antonio G. De Crisci antonio.decrisci ~ utoronto.ca wrote: > Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci-.-utoronto.ca] > Hello All, > > Has anybody used this program found at the link below? > > http://www.millsian.com/ > > Its still in development, but I like the idea of not using super computer for large system. It doesnt use the laws of QM, but yet is able to predict properties of organic molecules quite accurately using classical physics? > > Anthony> > > From owner-chemistry@ccl.net Tue Dec 16 15:46:00 2008 From: "Oscar Oscar.Ojeda*o*chemail.tamu.edu" To: CCL Subject: CCL: Nitroethane crystal structure Message-Id: <-38312-081216153859-2872-lph1d/9M5cpjiJA+e9QFsw]=[server.ccl.net> X-Original-From: Oscar Content-Type: multipart/alternative; boundary="------------050707020609030803050700" Date: Tue, 16 Dec 2008 14:00:43 -0600 MIME-Version: 1.0 Sent to CCL by: Oscar [Oscar.Ojeda(!)chemail.tamu.edu] This is a multi-part message in MIME format. --------------050707020609030803050700 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit Hi Emilio Thanks for your email. I'm looking for the actual nitroethane crystal structure ,by itself. Best Oscar Emilio José Juárez Pérez ejjuarez|*|icmab.es wrote: > Sent to CCL by: Emilio =?ISO-8859-1?Q?Jos=E9_Ju=E1rez_P=E9rez?= [ejjuarez:-:icmab.es] > Hello, > > Maybe I dont understand very well the question but the crystal > structures in the Cambridge Structural Database with refcodes : DAKROW, > DITGUI, DOJZOR, PIKHUM, QALNUK, TAXKUY, ZZZUXO and ZZZUXY contains > nitroethane as estructural solvent. > > > El lun, 15-12-2008 a las 18:49 -0500, Oscar U Ojeda > oscar.ojeda{=}chemail.tamu.edu escribió: > >> Sent to CCL by: "Oscar U Ojeda" [oscar.ojeda~~chemail.tamu.edu] >> Dear CCL peers; >> For some reason, the crystal structure of this solvent (EtNO2) seems to escape from traditional (ISI, CCSD, etc.) resource hits. I would appreciate any pointers. >> Cheers >> Oscar> >> > > ________________________________________________________________________ > > Emilio José Juárez-Pérez > PhD Student > ICMAB-CSIC > Campus UAB > 08193 Bellaterra (Barcelona) Spain. > ejjuarez::icmab.es > http://www.emiliojuarez.es > Tel. + 34 93 580 1853 (ext. 255) > Fax + 34 93 580 5729 > > ________________________________________________________________________> > > > > > > --------------050707020609030803050700 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit Hi Emilio
Thanks for your email. I'm looking for the actual nitroethane crystal structure ,by itself.
Best
Oscar


Emilio José Juárez Pérez ejjuarez|*|icmab.es wrote:
Sent to CCL by: Emilio =?ISO-8859-1?Q?Jos=E9_Ju=E1rez_P=E9rez?= [ejjuarez:-:icmab.es]
Hello,

Maybe I dont understand very well the question but the crystal
structures in the Cambridge Structural Database with refcodes : DAKROW,
DITGUI, DOJZOR, PIKHUM, QALNUK, TAXKUY, ZZZUXO and ZZZUXY contains
nitroethane as estructural solvent.


El lun, 15-12-2008 a las 18:49 -0500, Oscar U Ojeda
oscar.ojeda{=}chemail.tamu.edu escribió:
  
Sent to CCL by: "Oscar U Ojeda" [oscar.ojeda~~chemail.tamu.edu]
Dear CCL peers;
For some reason, the crystal structure of this solvent (EtNO2) seems to escape from traditional (ISI, CCSD, etc.) resource hits. I would appreciate any pointers.
Cheers
Oscar> 
    

________________________________________________________________________

Emilio José Juárez-Pérez
PhD Student
ICMAB-CSIC
Campus UAB
08193 Bellaterra (Barcelona) Spain.
ejjuarez::icmab.es
http://www.emiliojuarez.es
Tel.    + 34 93 580 1853 (ext. 255)
Fax    + 34 93 580 5729

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--------------050707020609030803050700-- From owner-chemistry@ccl.net Tue Dec 16 16:27:01 2008 From: "Antonio G. De Crisci antonio.decrisci+*+utoronto.ca" To: CCL Subject: CCL: Millsian 1.0 Message-Id: <-38313-081216162458-22222-uP6aqdJraeWRpjFrLF0hqg%%server.ccl.net> X-Original-From: "Antonio G. De Crisci" Date: Tue, 16 Dec 2008 16:24:53 -0500 Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci . utoronto.ca] Thanks for the warning, Nicholas! After a bit more background research and speaking to some of my colleagues, it seems I stumbled upon the tip of the iceberg with this program; I was not aware of the controversy behind the program and its creator(s), until today! Anthony > "Nicholas Labello label030++umn.edu" wrote: > > Sent to CCL by: Nicholas Labello [label030[#]umn.edu] > The theories that drive that program are not accepted by the greater > scientific community (or any scientific community that I am aware of). > The company (Black Light Power and/or Millsian, Inc.) posted a job offer > on the CCL list a few months ago and I looked into it a bit. After some > reading I became convinced that the program you asked about and parent > companies are in the absolute best light founded on misguided scientific > principles and at worst are simply fraudulent. Stay away from it. > Please see the "controversy" section in the following wiki: > http://en.wikipedia.org/wiki/Hydrino > > Nick > > > > Antonio G. De Crisci antonio.decrisci ~ utoronto.ca wrote: > > Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci-.-utoronto.ca] > > Hello All, > > > > Has anybody used this program found at the link below? > > > > http://www.millsian.com/ > > > > Its still in development, but I like the idea of not using super computer for large system. It doesnt use the laws of QM, but yet is able to predict properties of organic molecules quite accurately using classical physics? > > > > Anthony> > > > > > > From owner-chemistry@ccl.net Tue Dec 16 19:22:00 2008 From: "Brian Salter-Duke brian.james.duke~~gmail.com" To: CCL Subject: CCL: Millsian 1.0 Message-Id: <-38314-081216175317-29421-VQwyohoX4zQ0rJHxivgiLQ-*-server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 17 Dec 2008 09:52:56 +1100 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke-#-gmail.com] Nicholas Labello label030++umn.edu wrote: > > Sent to CCL by: Nicholas Labello [label030[#]umn.edu] > The theories that drive that program are not accepted by the greater > scientific community (or any scientific community that I am aware of). > The company (Black Light Power and/or Millsian, Inc.) posted a job offer > on the CCL list a few months ago and I looked into it a bit. After some > reading I became convinced that the program you asked about and parent > companies are in the absolute best light founded on misguided scientific > principles and at worst are simply fraudulent. Stay away from it. > Please see the "controversy" section in the following wiki: > http://en.wikipedia.org/wiki/Hydrino > > Nick I agree that this program is "not accepted by the greater scientific community (or any scientific community that I am aware of)". They do appear to be misguided. Nevertheless, I think we need to be clear why they appear to give such good results. I have been asked on wikipedia several times why there should not be an article on this program or a large section on it in one of the computational chemistry articles. There was an article but it was deleted at my suggestion. See http://en.wikipedia.org/wiki/Wikipedia:Articles_for_deletion/Millsian Brian. > > > Antonio G. De Crisci antonio.decrisci ~ utoronto.ca wrote: >> Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci-.-utoronto.ca] >> Hello All, >> >> Has anybody used this program found at the link below? >> >> http://www.millsian.com/ >> >> Its still in development, but I like the idea of not using super >> computer for large system. It doesnt use the laws of QM, but yet is >> able to predict properties of organic molecules quite accurately using >> classical physics? >> >> Anthonyhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Tue Dec 16 20:42:01 2008 From: "Alex Rudn rudikk99]=[yahoo.com" To: CCL Subject: CCL:G: solvent influence Message-Id: <-38315-081216204104-2911-OEzXQysQi+6tTPYIvgvH5Q!A!server.ccl.net> X-Original-From: "Alex Rudn" Date: Tue, 16 Dec 2008 20:41:00 -0500 Sent to CCL by: "Alex Rudn" [rudikk99**yahoo.com] Dear CClers, I want to compare mechanism of reaction in polar and nonpolar solvents. From experiments I know that in polar solvent we have 2 products while in nonpolar only one. for polar file I run %chk=CH3F_PS.chk %mem=6MW %nproc=1 # hf/3-21g freq=noraman Title Card Required 0 1 C H 1 B1 H 1 B2 2 A1 H 1 B3 2 A2 3 D1 F 1 B4 4 A3 2 D2 B1 1.07000000 B2 1.07000000 B3 1.07000000 B4 1.35000000 A1 109.47125080 A2 109.47121829 A3 109.47123134 D1 -120.00001416 D2 119.99998297 1 2 1.0 3 1.0 4 1.0 5 1.0 2 3 4 5 --Link1-- %chk=CH3F_PS # hf/3-21g SCF=Tight guess=read Geom=allCheck SCRF=(IPCM,Solvent=dichloromethane) for nonpolar solvent I run %chk=CH3F_PS.chk %mem=6MW %nproc=1 # hf/3-21g freq=noraman Title Card Required 0 1 C H 1 B1 H 1 B2 2 A1 H 1 B3 2 A2 3 D1 F 1 B4 4 A3 2 D2 B1 1.07000000 B2 1.07000000 B3 1.07000000 B4 1.35000000 A1 109.47125080 A2 109.47121829 A3 109.47123134 D1 -120.00001416 D2 119.99998297 1 2 1.0 3 1.0 4 1.0 5 1.0 2 3 4 5 --Link1-- %chk=CH3F_PS # hf/3-21g SCF=Tight guess=read Geom=allCheck SCRF=(IPCM,Solvent=toluene) With this type of input file for Gaussian I've got same Sum of electronic and thermal Enthalpies= -138.232041 and also I've got very similar summary Convergence Achieved. 1|1|UNPC-UNK|SP|RHF|3-21G|C1H3F1|PCUSER|16-Dec-2008|0||# HF/3-21G SCF= TIGHT GUESS=READ GEOM=ALLCHECK SCRF=(IPCM,SOLVENT=DICHLOROMETHANE)||Ti tle Card Required||0,1|C|H,1,1.07|H,1,1.07,2,109.47122063|H,1,1.07,2,1 09.47122063,3,-120.00001416,0|F,1,1.35,4,109.47122063,2,119.99998297,0 ||Version=x86-Win32-G03RevB.03|State=1-A1|HF=-138.286468|RMSD=6.712e-0 10|Dipole=0.466651,0.8082633,0.3298883|PG=C03V [C3(C1F1),3SGV(H1)]|| . Convergence Achieved. 1|1|UNPC-UNK|SP|RHF|3-21G|C1H3F1|PCUSER|16-Dec-2008|0||# HF/3-21G SCF= TIGHT GUESS=READ GEOM=ALLCHECK SCRF=(IPCM,SOLVENT=TOLUENE)||Title Card Required||0,1|C|H,1,1.07|H,1,1.07,2,109.47122063|H,1,1.07,2,109.47122 063,3,-120.00001416,0|F,1,1.35,4,109.47122063,2,119.99998297,0||Versio n=x86-Win32-G03RevB.03|State=1-A1|HF=-138.286468|RMSD=6.712e-010|Dipol e=0.466651,0.8082633,0.3298883|PG=C03V [C3(C1F1),3SGV(H1)]|| . And I've got similar results when I compare polar and nonpolar solvent calculations with both stable compound and transitional states. Am I looking at the wrong place? There must be energy difference otherwise how to explain different products with different solvents. At what energy should I look? Any answers are very welcome! Thank you very much in advance. P.S. happy holidays! Alex