From owner-chemistry@ccl.net Fri Feb 22 03:43:01 2008 From: "Andrzej Eilmes eilmes : chemia.uj.edu.pl" To: CCL Subject: CCL: CTTC V announcement Message-Id: <-36348-080221140458-15872-9D/I3oFj3niYCMV93Z1Luw]![server.ccl.net> X-Original-From: Andrzej Eilmes Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 21 Feb 2008 15:57:29 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Andrzej Eilmes [eilmes|,|chemia.uj.edu.pl] Dear CCL subscribers, Registration and abstract submission is now open for the Conference "Current Trends in Theoretical Chemistry V" which will take place in Krakow, Poland 6-10 July 2008. All information is available at the conference web page: http://www.chemia.uj.edu.pl/cttc5/ The conference is organized at the cetenary of the birthday and at the 25th anniversary of the death of Professor Kazimierz Guminski - the main initiator of theoretical chemistry research and teaching in Poland. He was the founder (in 1952) of the Theoretical Chemistry Department at the Jagiellonian University. All of you know at least one person who obtained M.Sc. in this department: the CCL maintainer, Jan Labanowski :-) The scope of the conference covers all aspects of quantum chemistry from theory and methodolgical developments to applications. The conference site will be the Faculty of Chemistry of the Jagiellonian University in Krakow. Krakow is one of the favourite tourist destinations in Europe owing to its historical monuments, cultural events and the night-life of the old city and the old Jewish town Kazimierz. BTW, CTTC V will take place immediately after this year edition of the famous Jewish Culture Festival. We are looking forward to welcoming you in Krakow in July, Andrzej Eilmes and Jacek Korchowiec, CTTC V Chairmen -- Current Trends in Theoretical Chemistry V 6-10 July 2008, Krakow, Poland http://www.chemia.uj.edu.pl/cttc5/ From owner-chemistry@ccl.net Fri Feb 22 04:23:01 2008 From: "Andreas Klamt klamt^cosmologic.de" To: CCL Subject: CCL: Self Consistent Reaction Field Message-Id: <-36349-080222032415-5176-MIm+GacTAQtbcqK5SQJpfQ ~ server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 22 Feb 2008 08:23:53 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt^^cosmologic.de] Sina, your problem is complicated. It must be split into two parts. 1) What is the right way to represent the ground-state of your molecule=20 in the protein environent, and 2) What is the best way to represent the the excitation in the presence=20 of the protein environment. to 1a) I doubt that dielectric solvation models are capable of doing=20 this. If you are able to do good Force-Field calculations on the=20 protein-ligand complex, perhaps do such first. 1b) Now could construct the ligand cavity of an SCRF model, remove the=20 ligand, use eps=3Dinfinity, i.e. a conductor, and calculate the screening= =20 charges of the exterior field. 1c) Now do the quantum chemical groundstate calculation of the ligand in = the presence of these fixed screening charges. Since these screening=20 charges represent the electrostatics of the protein exerted on the=20 ligand, this corresponds to a ground state calculation in the presence=20 of the protein field. 2) Now you can do the calculation of the UV spectrum by taking into=20 account the electronic polarizability of the protein represented by=20 eps=3Dn**2 which roughly is 2. Please note, that solvation by the=20 electronic polarizability - and only by the electronic polarizability)=20 is only required for the electronic density change by excitation, not=20 for the ground state density, because the slow reorientational degrees=20 of freedom cannot follow a fast electronic excitation as it is=20 considered in an UV spectrum. For more details on this see "Calculation of UV/Vis Spectra in Solution", A. Klamt, /J. Phys. Chem./=20 3349-3353 (1996). The problem is that this workflow is most likely nowhere implemented as=20 software. TURBOMOLE allows you do the excitation in the presence of the=20 frozen solute groundstate polarization charges, but step 1b) is not=20 supported and would have to be done externally (which is doable, because = the cavity and A-matrix are written to a file.) It might also be doable=20 with some MOPAC versions. Unfortunately, the last public domain versions = did not contain any robust COSMO implementation, nor the UV-extension. I = have a locally modified version of MOPAC7 which could do that. Perhaps=20 the new MOPAC2007 from Jimmy Stewart =20 (http://www.cacheresearch.com/mopac.html) can do it, but I do not know=20 exactly. As you see, this is real new research, not a standard application of=20 SCRF. Perhaps someone else has a simpler idea, but I doubt that the=20 problem can be casted into a simple SCRF problem. Andreas Sina T=FCreli sinatureli-x-gmail.com schrieb: > I just wanted to bring up my question once more since it was not=20 > answered. > > On Mon, Feb 18, 2008 at 5:17 AM, Sina T reli sinatureli-,-gmail.com=20 > > wrote: > > > Sent to CCL by: "Sina T reli" [sinatureli\a/gmail.com] > Greetings, > > I have a question about scrf. While calculationg UV-spectrum of > molecules, if we take them to be inside protein enviroment ligated > to some protein side-chain, is it a good idea to use scrf and if > it is what should be the index of refraction and dielectric > constant to be used? Since it is burried inside the protein I > assume a dielectric constant of 4-6 would be okay but I am not > sure about the refractive index. > > Thanks... > > > > > > > > > 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/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > --=20 -------------------------------------------------------------------------= ---- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt()cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------= ---- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------= ---- From owner-chemistry@ccl.net Fri Feb 22 05:52:02 2008 From: "Ewald Pauwels ewald.pauwels[*]ugent.be" To: CCL Subject: CCL:G: Isotropic and anisotropic spin couplings why are they not in output? Message-Id: <-36350-080222050259-14916-bUD/UDsjEOnS3wlj/oC4ew:_:server.ccl.net> X-Original-From: Ewald Pauwels Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 22 Feb 2008 10:17:56 +0100 MIME-Version: 1.0 Sent to CCL by: Ewald Pauwels [ewald.pauwels],[ugent.be] Dear Dimitri, For large structures (100 atoms or more), you should use Iop(6/82=1) in order to also print the (an)isotropic section. Sincerely, Ewald. Dimitri Svistunenko svist{}essex.ac.uk wrote: > Sent to CCL by: "Dimitri Svistunenko" [svist|a|essex.ac.uk] > G3 gives In the output file, G03 gives the Isotropic Fermi Contact Couplings listing, followed by the Spin Dipole Couplings and the Anisotropic Spin Dipole Couplings in Principal Axis System, when a B3LYP/6-31G* job is run on a small paramagnetic molecule (~40 atoms). When the same calculation is rum for a big structure (~200 atoms), these parts are missing in the output file. > > My question is should any keyword be present to have this output bits printed in the output file. Is it printed by default for small structures?> -- Ewald Pauwels Center for Molecular Modeling Ghent University Proeftuinstraat 86 B-9000 Gent Belgium http://molmod.ugent.be ewald.pauwels%a%UGent.be +32 9 264 65 76 From owner-chemistry@ccl.net Fri Feb 22 05:53:02 2008 From: "Syed T Moin tarisyed===yahoo.com" To: CCL Subject: CCL: Babel1.6 Message-Id: <-36351-080222052945-27225-McAE+cC9uK+BECo5KzrWHQ(-)server.ccl.net> X-Original-From: "Syed T Moin" Date: Fri, 22 Feb 2008 05:29:32 -0500 Sent to CCL by: "Syed T Moin" [tarisyed]|[yahoo.com] Hello, I am trying to install babal-1.6 on suse 10.2, but i m getting the following error, cc -O -c -o block.o block.c block.c: In function block__doalloc: block.c:102: error: incompatible types in assignment block.c:119: error: incompatible types in assignment make: *** [block.o] Error 1 kindly guide me Thanks in advance and regards From owner-chemistry@ccl.net Fri Feb 22 06:35:01 2008 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli[]gmail.com" To: CCL Subject: CCL: Self Consistent Reaction Field Message-Id: <-36352-080222062831-28729-zx73J/9iNTKeB127QqyPhA(-)server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_12718_16379142.1203679296060" Date: Fri, 22 Feb 2008 13:21:36 +0200 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli(-)gmail.com] ------=_Part_12718_16379142.1203679296060 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I see, if this is indeed not as simple as it seems I will try to follow you= r steps and also try to get more knowledge on the issue thanks for your answer On Fri, Feb 22, 2008 at 9:23 AM, Andreas Klamt klamt^cosmologic.de < owner-chemistry ~~ ccl.net> wrote: > > Sent to CCL by: Andreas Klamt [klamt^^cosmologic.de] > Sina, > > your problem is complicated. It must be split into two parts. > 1) What is the right way to represent the ground-state of your molecule > in the protein environent, > and > 2) What is the best way to represent the the excitation in the presence > of the protein environment. > > to 1a) I doubt that dielectric solvation models are capable of doing > this. If you are able to do good Force-Field calculations on the > protein-ligand complex, perhaps do such first. > 1b) Now could construct the ligand cavity of an SCRF model, remove the > ligand, use eps=3Dinfinity, i.e. a conductor, and calculate the screening > charges of the exterior field. > 1c) Now do the quantum chemical groundstate calculation of the ligand in > the presence of these fixed screening charges. Since these screening > charges represent the electrostatics of the protein exerted on the > ligand, this corresponds to a ground state calculation in the presence > of the protein field. > > 2) Now you can do the calculation of the UV spectrum by taking into > account the electronic polarizability of the protein represented by > eps=3Dn**2 which roughly is 2. Please note, that solvation by the > electronic polarizability - and only by the electronic polarizability) > is only required for the electronic density change by excitation, not > for the ground state density, because the slow reorientational degrees > of freedom cannot follow a fast electronic excitation as it is > considered in an UV spectrum. For more details on this see > "Calculation of UV/Vis Spectra in Solution", A. Klamt, /J. Phys. Chem./ > 3349-3353 (1996). > > The problem is that this workflow is most likely nowhere implemented as > software. TURBOMOLE allows you do the excitation in the presence of the > frozen solute groundstate polarization charges, but step 1b) is not > supported and would have to be done externally (which is doable, because > the cavity and A-matrix are written to a file.) It might also be doable > with some MOPAC versions. Unfortunately, the last public domain versions > did not contain any robust COSMO implementation, nor the UV-extension. I > have a locally modified version of MOPAC7 which could do that. Perhaps > the new MOPAC2007 from Jimmy Stewart > (http://www.cacheresearch.com/mopac.html) can do it, but I do not know > exactly. > > As you see, this is real new research, not a standard application of > SCRF. Perhaps someone else has a simpler idea, but I doubt that the > problem can be casted into a simple SCRF problem. > > Andreas > > > Sina T=FCreli sinatureli-x-gmail.com schrieb: > > I just wanted to bring up my question once more since it was not > > answered. > > > > On Mon, Feb 18, 2008 at 5:17 AM, Sina T reli sinatureli-,-gmail.com > > > > wrote: > > > > > > Sent to CCL by: "Sina T reli" [sinatureli\a/gmail.com] > > Greetings, > > > > I have a question about scrf. While calculationg UV-spectrum of > > molecules, if we take them to be inside protein enviroment ligated > > to some protein side-chain, is it a good idea to use scrf and if > > it is what should be the index of refraction and dielectric > > constant to be used? Since it is burried inside the protein I > > assume a dielectric constant of 4-6 would be okay but I am not > > sure about the refractive index. > > > > Thanks... > > > > > > > > > > > > > > > > > > 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/ > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > > > > > > -- > > -------------------------------------------------------------------------= ---- > Dr. habil. Andreas Klamt > COSMOlogic GmbH&CoKG > Burscheider Str. 515 > 51381 Leverkusen, Germany > > Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 > e-mail: klamt() cosmologic.de > web: www.cosmologic.de > > -------------------------------------------------------------------------= ---- > COSMOlogic > Your Competent Partner for > Computational Chemistry and Fluid Thermodynamics > > -------------------------------------------------------------------------= ---- > > > > - This is automatically added to each message by the mailing script -> > > ------=_Part_12718_16379142.1203679296060 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
I see, if this is indeed not as simple as it seems I will try to follo= w your steps and also try to get more knowledge on the issue
 
thanks for your answer

On Fri, Feb 22, 2008 at 9:23 AM, Andreas Klamt k= lamt^cosmologic.de <owner-chemistry ~~ ccl.net> wrote:

Sent to CCL by: Andreas Klam= t [klamt^^cosmologic.de= ]
Sina,

your problem is complicated. It must be split into two parts.<= br>1) What is the right way to represent the ground-state of your molecule<= br>in the protein environent,
and
2) What is the best way to represen= t the the excitation in the presence
of the protein environment.

to 1a) I doubt that dielectric solvation= models are capable of doing
this. If you are able to do good Force-Fiel= d calculations on the
protein-ligand complex, perhaps do such first.
1b) Now could construct the ligand cavity of an SCRF model, remove the
l= igand, use eps=3Dinfinity, i.e. a conductor, and calculate the screeningcharges of the exterior field.
1c) Now do the quantum chemical groundst= ate calculation of the ligand in
the presence of these fixed screening charges.  Since these screening<= br>charges represent the electrostatics of the protein exerted on the
li= gand, this corresponds to a ground state calculation in the presence
of = the protein field.

2) Now you can do the calculation of the UV spectrum by taking into
= account the electronic polarizability of the protein represented by
eps= =3Dn**2 which roughly is 2. Please note, that solvation by the
electroni= c polarizability - and only by the electronic polarizability)
is only required for the electronic density change by excitation, not
fo= r the ground state density, because the slow reorientational degrees
of = freedom cannot follow a fast electronic excitation as it is
considered i= n an UV spectrum. For more details on this see
"Calculation of UV/Vis Spectra in Solution", A. Klamt, /J. Phys. = Chem./
3349-3353 (1996).

The problem is that this workflow is mos= t likely nowhere implemented as
software. TURBOMOLE allows you do the ex= citation in the presence of the
frozen solute groundstate polarization charges, but step 1b) is not
supp= orted and would have to be done externally (which is doable, because
the= cavity and A-matrix are written to a file.) It might also be doable
with some MOPAC versions. Unfortunately, the last public domain versionsdid not contain any robust COSMO implementation, nor the UV-extension. Ihave a locally modified version of MOPAC7 which could do that. Perhaps the new MOPAC2007 from Jimmy Stewart
(http://www.cacheresearch.com/mopac.html= ) can do it, but I do not know
exactly.

As you see, this is r= eal new research, not a standard application of
SCRF. Perhaps someone else has a simpler idea, but I doubt that the
prob= lem can be casted into a simple SCRF problem.

Andreas


Sin= a T=FCreli sin= atureli-x-gmail.com schrieb:
> I just wanted to bring up my question once more since it was not
&g= t; answered.
>
> On Mon, Feb 18, 2008 at 5:17 AM, Sina T reli s= inatureli-,-gmail.com > <http://gmail.com> <owner-chemistry^-^= ccl.net
> <mailto:owner-chemistry%5E-%5Eccl.net>> wrote:
>
>
>     Sent to CCL by: "Sina  T  = ;reli" [sinatureli\a/gmail.com]
>     Greetings,
&g= t;
>     I have a question about scrf. While calculationg U= V-spectrum of
>     molecules, if we take them to be inside= protein enviroment ligated
>     to some protein side-chain, is it a good idea to use scr= f and if
>     it is what should be the index of refraction= and dielectric
>     constant to be used? Since it is burr= ied inside the protein I
>     assume a dielectric constant of 4-6 would be okay but I = am not
>     sure about the refractive index.
>
&g= t;     Thanks...
>
>
>
>
>
><= br>>
>
>     E-mail to subscribers: CHEMISTRY^-^ccl.net
>     <mailto:CH= EMISTRY%5E-%5Eccl.net> or use:>
>     E-mail to a= dministrators: CHEMISTRY-REQUEST^-^ccl.net
>     <mailto:CHEMISTRY-REQUEST%5E-%5Eccl.net> or use&g= t;     Conferences:
>     http://server.ccl.net/chemistry/announceme= nts/conferences/
>
>     Search Messages: http://www.ccl.net/htdig  (login: ccl, Password:
>     search)>
>
>


--
-----------= ------------------------------------------------------------------
Dr. h= abil. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
= 51381 Leverkusen, Germany

Tel.: +49-2171-73168-1  Fax:  +49-2171-73168-9
e-mail: kla= mt() cosmologic.de<= br>web:    www.cosmologic.de
---------------------------------------------------------------------------= --
COSMOlogic
      Your Competent Partner for
&nbs= p;     Computational Chemistry and Fluid Thermodynamics
------= -----------------------------------------------------------------------



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------=_Part_12718_16379142.1203679296060-- From owner-chemistry@ccl.net Fri Feb 22 07:07:01 2008 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas[#]chem.elte.hu" To: CCL Subject: CCL:G: Fixing MM atoms in ONIOM Message-Id: <-36353-080222061844-19318-L5MbiNvLYfx2kp/G8NBI0Q===server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 21 Feb 2008 23:08:11 +0100 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas(~)chem.elte.hu] Hi Chunyi, You should send the input file as I cannot see any direct indication for an error. It is also necessary to know, how many atoms were frozen and which version of Gaussian of Gaussian was used in the study. Good luck, Ödön On Sat, 2008-02-16 at 23:48 -0500, Chun-Yi Sung juneyi1^_^yahoo.com.tw wrote: > Sent to CCL by: "Chun-Yi Sung" [juneyi1:_:yahoo.com.tw] > Hi, CCLers > > I tried to fix MM atoms in ONIOM like this: > Si-Si3 -1 3.063865 -6.363456 10.491696 L > > and for the QM atoms I wanted to fix, I flagged them with 0 like this: > Si-Si3 0 -3.978982 4.068174 2.511722 H > but then I used "X n F" at the end along with "opt=modredundant" in the > Route section. > > However, in the output file, I got a huge block of stuff like this: > NRF= 0 NRA= 0 NVA= 0 HaveQM=F > Convergence limit is 0.300E-04 MaxStp= 5000 StMxLn= 1.00D-04 StpMin= 1.00D-06. > Convergence criteria 0.00004500 0.00003000 0.00018000 0.00012000 > Step NS ND Rises OKQ Scale Max. Force RMS Force Max. Disp. RMS Disp. Energy Flag > 1 0 0 F T 1.00D+00 0.00000000 NaNQ 0.00000000 NaNQ -0.0450025 +-+- > NRF= 0 NRA= 0 NVA= 0 HaveQM=F > Convergence limit is 0.300E-04 MaxStp= 5000 StMxLn= 1.00D-04 StpMin= 1.00D-06. > Convergence criteria 0.00004500 0.00003000 0.00018000 0.00012000 > Step NS ND Rises OKQ Scale Max. Force RMS Force Max. Disp. RMS Disp. Energy Flag > 1 0 0 F T 1.00D+00 0.00000000 NaNQ 0.00000000 NaNQ -0.0450025 +-+- > > during each geom optimization step, and I always have "NaNQ" for the > RMS for MM Force like this: > Item Value Threshold Converged? > Maximum Force 0.064776 0.000450 NO > RMS Force 0.006255 0.000300 NO > Maximum Displacement 0.164584 0.001800 NO > RMS Displacement 0.013024 0.001200 NO > Maximum MM Force 0.000000 0.000045 YES > RMS MM Force NaNQ 0.000030 YES > > My questions are: > > 1. Did I fixed the MM atoms in the correct way? If not, what is the > correct way? > 2. If I did fix MM atoms correctly, is it normal to have the block > shown above and NaNQ for RMS for MM Force ? and is there any command > I can use so that it won't output the huge block shown above? > > > thanks > > Chunyi> > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Fri Feb 22 07:42:00 2008 From: "Pablo Albores albores=-=qi.fcen.uba.ar" To: CCL Subject: CCL:G: LNMO in G03 Message-Id: <-36354-080222055925-5172-haKAV/2B9LYv4gwhJ92Rbw- -server.ccl.net> X-Original-From: "Pablo Albores" Date: Fri, 22 Feb 2008 05:59:21 -0500 Sent to CCL by: "Pablo Albores" [albores::qi.fcen.uba.ar] Hi, I am trying to generate natural localized molecular orbitals (NLMO) with gaussian03 (NBO 3.1), for some model simple coordination compounds using the following combination of keywords: Pop=(NBORead,SaveNLMOs) and after the input section: $NBO AONLMO $END However after computing the NBO, I received the following error message while program attempts to compute the NLMO: "....NATURAL LOCALIZED MOLECULAR ORBITAL (NLMO) ANALYSIS: Highest occupied NBOs are not at the beginning of the NBO list; The NLMO program is not currently set up to handle this. Illegal range for read: IUnit= 7 Address= -128 Length= -128 File length= 235520. Error termination in NtrErr: NtrErr called from NtrIO. ...." Do someone have any clue of whats going on, is just really an intrinsic limitation of the NBO module or is there something that could be do to solve the problem? Thanks, in advance, Dr. Pablo Albors Humboldt Post-Doctoral Fellow Johannes Gutenberg - University of Mainz Institute of Inorganic and Analytical Chemistry Duesbergweg 10-14 D-55128 Mainz-Germany Phone +49 6131 / 39-25377 Fax +49 6131 / 39-23922 From owner-chemistry@ccl.net Fri Feb 22 08:25:01 2008 From: "Val Gillet v.gillet^sheffield.ac.uk" To: CCL Subject: CCL: Short Course: Practical Introduction to Chemoinformatics Message-Id: <-36355-080222082004-21183-IknmhraDRfwvbOmEBWl+qw|server.ccl.net> X-Original-From: "Val Gillet" Date: Fri, 22 Feb 2008 08:20:00 -0500 Sent to CCL by: "Val Gillet" [v.gillet-,-sheffield.ac.uk] "A Practical Introduction to Chemoinformatics" June 17th-20th 2008 The University of Sheffield will be hosting the above short course which is supported by the Chemical Structure Association Trust (CSAT) and the Molecular Graphics and Modelling Society (MGMS). This intensive short course, which has been run on an annual basis since 2000, provides an introduction to the major aspects of Chemoinformatics, with particular emphasis on applications in modern drug discovery. The course will comprise a mixture of hands-on workshops using state-of-the-art software, lectures, and informal discussions and will be delivered by world leaders in the field from academia and industry. Please note that places on the course are limited to 18. Two student bursaries will be available thanks to generous support provided by the CSAT and the MGMS. Details on how to apply for these are available on the website. For further details see: http://cisrg.shef.ac.uk/chemcourse or contact Val Gillet (v.gillet*sheffield.ac.uk) From owner-chemistry@ccl.net Fri Feb 22 11:16:00 2008 From: "Jerome Kieffer jerome.Kieffer * terre-adelie.org" To: CCL Subject: CCL: Computing on graphical processors Message-Id: <-36356-080222074411-27256-PDFeIg+A/R0l5puyy2AnmA()server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Fri, 22 Feb 2008 12:45:35 +0100 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer-x-terre-adelie.org] Nice paper ... Have you made some tests on QM codes ? because 1GB of memory is really tinny for QM. Best regards. --=20 J=E9r=F4me KIEFFER : http://www.terre-adelie.org From owner-chemistry@ccl.net Fri Feb 22 14:03:00 2008 From: "Sahan Thanthiriwatte sahanchem-,-gmail.com" To: CCL Subject: CCL:G: What QM-Code/Basis-Set for looking at reactions on a metal surface Message-Id: <-36357-080221164215-6332-gWlfLFT5a0AoDbfxHml3xw%x%server.ccl.net> X-Original-From: Sahan Thanthiriwatte Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=KOI8-R; format=flowed Date: Thu, 21 Feb 2008 14:51:48 -0500 MIME-Version: 1.0 Sent to CCL by: Sahan Thanthiriwatte [sahanchem-$-gmail.com] Hi Roger, You can try VASP. Kanchana -------------------- Kanchana S. Thanthiriwatte Department of Chemistry and HPCC Center for Computational Sciences, Mississippi State University Box 9573 Mississippi State, MS 39762 (Tel) 662-325-4633 (Fax) 662-325-1618 Roger Kevin Robinson r.robinson{=}imperial.ac.uk wrote: > > Sent to CCL by: Roger Kevin Robinson [r.robinson]*[imperial.ac.uk] > Dear All, > > Previously I've been using Gaussian to look at reaction paths for > organic molecules in the gas phase. > > A colleague of mine is interested in Activation Energies for the > rearrangements of organic molecules whist bound to a metal surface. > > I did some quick calculations for him for the respective reactions in > the gas phase, with out considering the metal, to get a basic starting > point. > > They now need some more accurate numbers. I've never done any > calculations on a metal surface before so I'm a bit lost. > > First of all I tried the same attaching the organic molecule to a single > platinum atom. The only basis set I could find for which the Atomic > number of platinum was not out of range were lanl2mb and lanl2dz. > > I also tried building a platinum cluster and minimising with > b3lyp/lanl2mb and b3lyp/lanl2dz this is taking a long time. Obliviously > UFF MM can also be used. > > I then decided to search the literature, most of the QM work on metal > surface seems to be using different QM codes from Gaussian such as > Castep. Although a lot of the work seems to be using DFT functionals, > such as B3LYP, which I am familiar with, the Basis sets are unknown to me. > > Is it feasible to study reactions on a surface using Gaussian ? Should I > start to look at another QM code ? Or should I be looking for other > basis sets to use in Gaussian ? > > This is not my main work so I dont want to be spending too much time on > it. Also if I am working with a 9 atom platinum cluster approximately > how long would I be looking at for calculations times ? > > Any other help or advice appreciated. > > Thanks > > Rogerhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Fri Feb 22 14:37:01 2008 From: "D. Boyd boyd###chem.iupui.edu" To: CCL Subject: CCL: running SYBYL via a Mac Message-Id: <-36358-080222120402-25849-4SIkQgTnrMuCjQ9ThXSLHg|server.ccl.net> X-Original-From: "D. Boyd" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Fri, 22 Feb 2008 12:03:53 -0500 Mime-Version: 1.0 (Apple Message framework v624) Sent to CCL by: "D. Boyd" [boyd,+,chem.iupui.edu] Hi, Although Tripos does not support the Macintosh platform for its SYBYL molecular modeling system, I have been told that it is possible use a Mac as a GUI for SYBYL running on a UNIX server. The steps are roughly as follows: Open x11 on the Mac At $ prompt, enter xhost + Use ssh to open a secure shell At % prompt, enter env_DISPLAY_IP# Enter SYBYL We have tried various versions of this procedure, but have not hit upon anything that worked. Does anyone have experience running SYBYL > from a Mac running OS 10.3.9? Thanks, Don From owner-chemistry@ccl.net Fri Feb 22 15:12:01 2008 From: "Eve G Zoebisch eve(_)ripariansoftware.com" To: CCL Subject: CCL: D=4, not 2. Can anyone find an error in this equation? Message-Id: <-36359-080222143153-23354-D4wf5evuzSHrKN9jYUzeHQ|a|server.ccl.net> X-Original-From: "Eve G Zoebisch" Date: Fri, 22 Feb 2008 14:31:49 -0500 Sent to CCL by: "Eve G Zoebisch" [eve{}ripariansoftware.com] Below is analysis for two charges in dielectric material. It is very simple, only 4 lines, yet the result does not agree with the equation used in force fields. It shows that permittivity to the second power should be in the denominator of the electrostatic term (e.g. D=4), whereas force fields use permittivity to the first power (e.g. D=2). Analysis: A point charge, q, in dielectric induces a charge about it. Textbook examples show that the point charge plus its induced charge has a total charge of q/p, where p is the permittivity. To calculate the total interaction energy between two sets of charges, the charges are multiplied and divided by the distance. E=K(q/p)(q/p)/r =Kqq/p^2r where K is a constant reflecting units and conventions. p is used for permittivity instead of epsilon since email does not have an epsilon character. For the textbook solution of the point charge in dielectric see Lorrain and Corson, equation 3.76 on page 113. (www.ripariansoftware.com/Lorrain&Corson111-113.pdf ) To translate from physics language to chemistry language: Qnet is total charge, both initial and induced. The bound charge concept in physics is called induced charge in chemistry and a free charge in physics, Q, is equivalent to the chemistry partial charge. Epsilon is the permittivity of the dielectric material. Pardon me for taking the bandwidth, however a reviewer asserted without proof that the science is wrong and further asserted that someone else should figure out why the science is wrong. In light of how important it is to use the correct equation, I am opening the discussion to the comp chem community to see if anyone can find an error in the analysis. COMMENTS TO DATE AND REBUTTALS This is so well worked out; there couldnt possibly be a problem. Physics textbooks provide analysis for the problems that physicists solve. I have not seen an equation for force fields in textbooks, nor have I seen a derivation in the literature. In force fields, a partial charge and the charge it induces interacts with another partial charge combined with its induced charge. The interaction between the two sets of charges is the term that is needed. Its Coulombs Law. All the physics textbooks I have seen provide the original version of Coulombs Law (see Jackson, Corson and Lorrain, Halliday and Resnick, and Landau and Lipshitz ). Dielectric permittivity is not in the equation. There is a permittivity version of Coulombs Law ( for example see page 7 of www.ripariansoftware.com/DielectricProperties_pg7-8.pdf ) where the permittivity appears in the denominator to the first power. In the section titled, The properties of the electromagnetic vectors, in the first half of the second paragraph, it appears that the permittivity version of Coulombs Law is the correct version to use for force fields. However, in the second half of the paragraph the text defines the electrostatic field as the force acting on a small charge, i.e. a probe charge that does not induce a charge about it. While there is no a-priori reason to think the probe charge refers to the Coulomb equation above it; when I consider Gauss Law, superposition of electrostatic field, and vector calculus, the only interpretation that is consistent is that the probe charge refers to the first half of the paragraph as well as the second. Physicists whose professional integrity is not endangered assert that it is obvious that the probe charge refers to the first half; That is how physicists think. Albeit, they are friends of mine and I suspect they are biased. Logically the force acting on a probe charge is not the same as the force acting on a normal charge. Since the definition of the electrostatic field is based on a probe charge, the probe charge version of the force equation must be used. This is a logical interpretation of the text; however this interpretation is too convoluted to be satisfying. You arent supposed to have a term for the interaction between the two sets of induced charge. Traditionally, all terms must be included. It is unusual to set a non-trivial term to zero. To be honest, Ive never seen this done before. The charges are not actually reduced, although the electrostatic field due to their presence is reduced. Gauss Law relates the total charge in a volume with the surface integral of the electrostatic field. Physics textbooks are loaded with examples of how the electrostatic field is integrated to determine net charge. If the electrostatic field is reduced, the total charge must have been reduced. (for discussion on total charge, see Lorrain and Corson, page 105, Section 3.6 (www.ripariansoftware.com/Lorrain&Corson_pg104-109.pdf). When you divide one side of Gauss Law by a constant, you arent supposed to divide the other side by that constant. Electrostatic field and total charge are directly related to each other, i.e. the charge generates the electrostatic field. A change in one implies a change in the other. That is the point of Gauss Law. From owner-chemistry@ccl.net Fri Feb 22 16:39:00 2008 From: "Starr Hazard hazards^musc.edu" To: CCL Subject: CCL: running SYBYL via a Mac Message-Id: <-36360-080222162431-10680-P0GL1OO8xxROfCAbCpILZA ~ server.ccl.net> X-Original-From: Starr Hazard Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 22 Feb 2008 15:47:53 -0500 MIME-Version: 1.0 Sent to CCL by: Starr Hazard [hazards[]musc.edu] I regularly use a MAC to connect to a server to run SYBYL. I use secureshell and the X11 server. I open an X11 window on the MAC At the prompt I type ssh -Y username:+:host.somewhere.edu This opens an X-connection to the server. After site-dependent initialization commands (ours are setsybyl and then sybyl)the SYBYL graphics GUI opens, works and provides excellent graphics with ribbons and solid surface representations that are excellent. The three-button mouse emulation is awkward but usable. This is not an officially sanctioned method but it does work on our system. This is using MAC OSX version 10.4.11 Starr --On Friday, February 22, 2008 12:03 PM -0500 "D. Boyd boyd###chem.iupui.edu" wrote: > > Sent to CCL by: "D. Boyd" [boyd,+,chem.iupui.edu] > Hi, > Although Tripos does not support the Macintosh platform for its SYBYL > molecular modeling system, I have been told that it is possible use a > Mac as a GUI for SYBYL running on a UNIX server. > > The steps are roughly as follows: > Open x11 on the Mac > At $ prompt, enter xhost + > Use ssh to open a secure shell > At % prompt, enter env_DISPLAY_IP# > Enter SYBYL > > We have tried various versions of this procedure, but have not hit upon > anything that worked. Does anyone have experience running SYBYL >> from a Mac running OS 10.3.9? > > Thanks, Donhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Fri Feb 22 18:14:01 2008 From: "mustafa emirik mustafaemirik|*|hotmail.com" To: CCL Subject: CCL:G: gaussian03 error message 2070 Message-Id: <-36361-080222181022-12959-bZMeoVZlwuoNRB7XLCznmw!A!server.ccl.net> X-Original-From: "mustafa emirik" Date: Fri, 22 Feb 2008 18:10:18 -0500 Sent to CCL by: "mustafa emirik" [mustafaemirik###hotmail.com] dear CCL subscribers I have run gaussian 03 cbs-qb3 for pka calculation but calculation ended with error message after this step; #N Geom=AllCheck Guess=Read SCRF=Check QCISD(T)/6-31+G(d') before the error message always display that " **** Warning!!: The largest alpha MO coefficient is 0.15740897D+03 Estimate disk for full transformation 1445218449 words. Semi-Direct transformation. Bad length for file. FileIO: IOper= 0 IFilNo(1)= 201 Len= -1369672788 IPos= 0 Q= 6424808 dumping /fiocom/, unit = 1 NFiles = 73 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 62443008 FType=2 FMxFil=10000 " what is the wrong I couldn't understand. please help me. thans to all of you all the best From owner-chemistry@ccl.net Fri Feb 22 18:48:01 2008 From: "Reichert, David reichertd|*|mir.wustl.edu" To: CCL Subject: CCL: running SYBYL via a Mac Message-Id: <-36362-080222180450-11312-d/wH0Lt4Jgjp6vwyQeVkaw[]server.ccl.net> X-Original-From: "Reichert, David" Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 22 Feb 2008 16:34:49 -0600 MIME-Version: 1.0 Sent to CCL by: "Reichert, David" [reichertd%mir.wustl.edu] Don, I use a mac to work with Sybyl on an SGI almost everyday and it works fine.= Your mixing together a couple of approaches which is probably why it isn't= working. If you connect via telnet then On mac: xhost+ Then telnet to unix box, login and setenv DISPLAY IP:0.0 If you connect to the unix box via ssh then ssh -X username|-|unixbox_IP, The -X allows for X11 tunneling. Hope that helps, -dave David E. Reichert Asst. Professor of Radiology Washington University School of Medicine e-mail: reichertd|-|wustl.edu voice: 314-362-8461 fax: 314-362-9940 web: http://scoobie.wustl.edu/ -----Original Message----- > From: owner-chemistry|-|ccl.net [mailto:owner-chemistry|-|ccl.net] Sent: Friday, February 22, 2008 11:04 AM To: Reichert, David Subject: CCL: running SYBYL via a Mac Sent to CCL by: "D. Boyd" [boyd,+,chem.iupui.edu] Hi, Although Tripos does not support the Macintosh platform for its SYBYL molecular modeling system, I have been told that it is possible use a Mac as a GUI for SYBYL running on a UNIX server. The steps are roughly as follows: Open x11 on the Mac At $ prompt, enter xhost + Use ssh to open a secure shell At % prompt, enter env_DISPLAY_IP# Enter SYBYL We have tried various versions of this procedure, but have not hit upon anything that worked. Does anyone have experience running SYBYL > from a Mac running OS 10.3.9? Thanks, Don -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThe materials in this message are private and may contain Protected Healthc= are Information. If you are not the intended recipient, be advised that an= y unauthorized use, disclosure, copying or the taking of any action in reli= ance on the contents of this information is strictly prohibited. If you ha= ve received this email in error, please immediately notify the sender via t= elephone or return mail. From owner-chemistry@ccl.net Fri Feb 22 22:00:00 2008 From: "Kalju Kahn kalju _ chem.ucsb.edu" To: CCL Subject: CCL: running SYBYL via a Mac Message-Id: <-36363-080222215730-29233-pCM3kiOP07ZRWnqrsCr+yQ(a)server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 22 Feb 2008 18:56:31 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju/./chem.ucsb.edu] Don, I do not have a Mac around but I recall it working well with SGI as server and Mac (early PowerPC?) as the client. I believe that one thing that was needed in this setup was to switch from default OGLX mode to the XDEV graphisc mode (SYBYL command: TERMINAL XDEV). Hope this helps, Kalju > > Sent to CCL by: "D. Boyd" [boyd,+,chem.iupui.edu] > Hi, > Although Tripos does not support the Macintosh platform for its SYBYL > molecular modeling system, I have been told that it is possible use a > Mac as a GUI for SYBYL running on a UNIX server. > > The steps are roughly as follows: > Open x11 on the Mac > At $ prompt, enter xhost + > Use ssh to open a secure shell > At % prompt, enter env_DISPLAY_IP# > Enter SYBYL > > We have tried various versions of this procedure, but have not hit upon > anything that worked. Does anyone have experience running SYBYL >> from a Mac running OS 10.3.9? > > Thanks, Don> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106