From owner-chemistry@ccl.net Thu Aug 6 02:21:00 2009 From: "Fedor Goumans fedor.goumans=-=googlemail.com" To: CCL Subject: CCL:G: Gaussian's Hessian matrix Message-Id: <-39932-090805160255-31917-KFVCTcC3yMw1iONrmBIlNw^server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 5 Aug 2009 21:30:24 +0200 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [fedor.goumans^_^googlemail.com] Hi Hoa Nguyen, These are in atomic units, i.e. Hartree/bohr^2 and are not yet mass-weighte= d. Remember that if you diagonalise the mass-weighted Hessian the frequencies you will get out will also be in atomic time units (sqrt (amu.bohr^2/Hartree)) which you probably want to convert to cm-1. Hope this helps, Fedor 2009/8/5 Hoa Nguyen hoa_giao_nguyen[a]yahoo.com : > Hi, > Does anyone know the unit of the Hessian Matrix in the check point file o= f a > Gaussian calculation (it is called=A0Cartesian Force Constants)? > I think it must be Hartree/Angstrom^2. However when I diagonalized the > matrix to obtain vibrational frequency (I follow the paper "Vibrational > Analysis in Gaussian" from Dr Ochterski), I cannot get the same frequenci= es > like the Gaussian results. > Thanks, > Hoa Nguyen > --- On Sat, 10/4/08, Gennady L Gutsev gennady.gutsev_+_famu.edu > wrote: > > From: Gennady L Gutsev gennady.gutsev_+_famu.edu > Subject: CCL:G: G03 on Barcelona's > To: "Nguyen, Hoa G " > Date: Saturday, October 4, 2008, 8:39 PM > > > Sent to CCL by: "Gennady L Gutsev" [gennady.gutsev/a\famu.edu] > > Hi everybody, > > we have installed a cluster of 50 Barcelona's but Gaussian jobs > are not running. If I submit, say, 10 jobs, 5 die in a few seconds, > 2 in a few minutes, 3 in hours to several days. > =A0=A0=A0Have anybody experienced similar problems? I wonder what could b= e > wrong: or processors themselves, either G03 is not well adapted to > the Barcelona platform, either the problem with the system support? > =A0=A0=A0The company we purchased the cluster from is Western Scientific = (CA). > Can anybody say a good word about this company? > =A0 =A0 Thank you all. > Gennady > > > > -=3D This is automatically added to each message by the mailing script = =3D-the > strange characters on the top line to the : sign. You can also> > E-mail to subscribers: CHEMISTRY:ccl.net or use: > =A0 =A0 =A0> > E-mail to administrators: CHEMISTRY-REQUEST:ccl.net or use > =A0 =A0 =A0> =A0 =A0 =A0> > Search Messages: http://www.ccl.net/htdig=A0 (login: ccl, Password: searc= h)> =A0 =A0 =A0> > > > From owner-chemistry@ccl.net Thu Aug 6 04:25:01 2009 From: "Marcel Swart marcel.swart : icrea.es" To: CCL Subject: CCL: ORCA - error termination in ORCA_GTOInt Message-Id: <-39933-090806041208-4922-ACmfJyx2cosa2xrBDjPePw!A!server.ccl.net> X-Original-From: Marcel Swart Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 6 Aug 2009 10:10:02 +0200 MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart_._icrea.es] Add the directory where ORCA executables are located to your path, it depends on your shell (csh, tcsh, bash, ..) how you should do this. Since it is the "sh" that is complaining that it can not find an exe, probably it should be placed in $HOME/.profile like this export ORCA_DIR=3DXXXXXXXXXX export PATH=3D$PATH:$ORCA_DIR where of course instead of XXXXXXXX you should put the name of the directory with all the ORCA executables. Hope this helps. Quoting "Rommel B Viana rommelbv^-^yahoo.com.br" : > > Sent to CCL by: "Rommel B Viana" [rommelbv+*+yahoo.com.br] > Dear CCL > > I performed a calculation and find an error. I am runing the =20 > calculation in the same directory of the executables, to make sure =20 > that programs can call each other.Could anyone suggest a way out, or =20 > point me to my error? > Thanks, > Rommel B. Viana > > > =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=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D > INPUT FILE > =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=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D > NAME =3D co.inp > | 1> # > | 2> # > | 3> # > | 4> %method method HF > | 5> ProgSCF "orca_scf.exe" > | 6> ProgGTOInt "orca_gtoint.exe" > | 7> end > | 8> ! noautostart > | 9> %basis basis SV > | 10> end > | 11> * xyz 0 1 > | 12> C 0 0 0 > | 13> O 0 0 1.13 > | 14> * > | 15> > | 16> ****END OF INPUT**** > =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=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D > > **************************** > * Single Point Calculation * > **************************** > > --------------------------------- > CARTESIAN COORDINATES (ANGSTROEM) > --------------------------------- > C 0.000000 0.000000 0.000000 > O 0.000000 0.000000 1.130000 > > ---------------------------- > CARTESIAN COORDINATES (A.U.) > ---------------------------- > NO LB ZA FRAG MASS X Y Z > 0 C 6.0000 0 12.011 0.000000 0.000000 0.000000 > 1 O 8.0000 0 15.999 0.000000 0.000000 2.135391 > > -------------------------------- > INTERNAL COORDINATES (ANGSTROEM) > -------------------------------- > C 0 0 0 0.000000 0.000 0.000 > O 1 0 0 1.130000 0.000 0.000 > > --------------------------- > INTERNAL COORDINATES (A.U.) > --------------------------- > C 0 0 0 0.000000 0.000 0.000 > O 1 0 0 2.135391 0.000 0.000 > > --------------------- > BASIS SET INFORMATION > --------------------- > There are 2 groups of distinct atoms > > Group 1 Type C : 7s4p contracted to 3s2p pattern {511/31} > Group 2 Type O : 7s4p contracted to 3s2p pattern {511/31} > > Atom 0C basis set group =3D> 1 > Atom 1O basis set group =3D> 2 > sh: orca_gtoint.exe: command not found > ORCA finished by error termination in ORCA_GTOInt > ORCA finished by error termination in ORCA_GTOInt > > > > -=3D This is automatically added to each message by the mailing script =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 dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart,icrea.es marcel.swart,udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =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 From owner-chemistry@ccl.net Thu Aug 6 05:00:01 2009 From: "Harald Lanig harald.lanig{:}chemie.uni-erlangen.de" To: CCL Subject: CCL: Model(l)ing'09 in Erlangen, Germany: Registration Open Until August 31st Message-Id: <-39934-090806043938-12276-TKvr1ucxdEPwchspAzMhDQ#,#server.ccl.net> X-Original-From: Harald Lanig Content-Disposition: inline Content-Type: text/plain; charset="US-ASCII"; format="flowed" Date: Thu, 6 Aug 2009 10:38:19 +0200 MIME-Version: 1.0 Sent to CCL by: Harald Lanig [harald.lanig*_*chemie.uni-erlangen.de] Dear List Subscribers, A Molecular Graphics and Modelling Society (MGMS) International Meeting will take place in Erlangen, Germany from September 7th (registration and mixer) to 11th 2009. The meeting will be preceded by the annual Molecular Modelling Workshop organised by the MGMS German Section from Sunday 6th to Monday, September 7th. Model(l)ing'09 is also a celebration of Tim Clark's 60th birthday. Important notice: Although we reached the deadline for submitting abstracts for poster and oral contributions, we still have a few speaker slots for the Modeling Workshop on Sunday/Monday free! So please continue to submit your Workshop contribution! Additionally, we continue to accept your registration for the Modeling Workshop and Model(l)ing'09 until August 31st! For information about the meeting and invited speakers please visit: http://www.modeling09.com Hope to see you in Erlangen soon! -Harald Lanig -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 harald DOT lanig AT chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.chemie.uni-erlangen.de/lanig Visit Erlangen - join us at Model(l)ing 2009 http://www.modeling09.com ------------------------------------------------------------------------ From owner-chemistry@ccl.net Thu Aug 6 05:27:01 2009 From: "Serdar Badošlu sbadoglu%a%gazi.edu.tr" To: CCL Subject: CCL: How to calculate a bond energy Message-Id: <-39935-090806043824-11784-TFPeJ0+EdcouhC4YMZkPHg##server.ccl.net> X-Original-From: "Serdar Badošlu" Date: Thu, 6 Aug 2009 07:35:13 -0000 Sent to CCL by: "Serdar Badošlu" [sbadoglu+*+gazi.edu.tr] Dear Eduardo, Binding energy can be calculated as the energy of the whole molecule minus the sum of the energies of the isolated sub-units. But keep in mind that this is a basic approximation and may not give satisfactory results. Regards, Serdar Badoglu "Eduardo Lemos de Sa edulsa*o*quimica.ufpr.br" dedi: > > Sent to CCL by: "Eduardo Lemos de Sa" [edulsa#%#quimica.ufpr.br] > Sirs and Ladies > > I have a silly questions: how can I calculate a energy rising from a bond > between two atoms in a organic molecule? I guess that the answer can be: > calculate the SCF energy for the whole molecule, for two radicals > originated from the dissociation. Thus, bound energy would be: sum (SCF > energy for radicals) - SCF energy for the complete molecule. Am I right? > > Thank you in advance > > Yours > > Eduardo > > > > > > -- > Eduardo Lemos de Sa > edulsa*_*quimica.ufpr.br > Professor Assoc. II - Departamento de Quimica > Universidade Federal do Parana > C. P. 19081 > 81531-990 Curitiba/PR - Brazil > Fone (41) 3361 3300> > > From owner-chemistry@ccl.net Thu Aug 6 06:03:01 2009 From: "Stan van Gisbergen vangisbergen _ scm.com" To: CCL Subject: CCL: energies of chemical bonds Message-Id: <-39936-090806040350-21289-6b+P/mbCMAU+jTA7HBNePg|a|server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-105-652326862 Date: Thu, 6 Aug 2009 09:07:46 +0200 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Stan van Gisbergen [vangisbergen*o*scm.com] --Apple-Mail-105-652326862 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Dr. Abdelghani, The current ADF2008 release contains the well-known bond energy decomposition based on ADF's fragment approach: http://www.scm.com/Products/Overview/bondenergy.html The ADF2009 release, which is in preparation, will also contain the new powerful ETS-NOCV scheme: M. Mitoraj, A. Michalak and T. Ziegler, Chem. Theory Comput., 5 (2009), 962 M. Mitoraj, A. Michalak and T. Ziegler, Organometallics, 28 (2009), 3727 Best regards, Stan van Gisbergen On Aug 5, 2009, at 10:52 AM, may abdelghani may01dz ~ yahoo.fr wrote: > Dear CCL's > > How I can calculate the energies of chemical bonds, in ADF > > thank you very much, > > Dr. S.J.A. van Gisbergen Chief Executive Officer Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen---scm.com http://www.scm.com T: +31-20-5987626 F: +31-20-5987629 --Apple-Mail-105-652326862 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=US-ASCII
Dear Dr. = Abdelghani, 

The current ADF2008 release contains the well-known bond energy = decomposition based on ADF's fragment approach: =  
http://www.s= cm.com/Products/Overview/bondenergy.html

The ADF2009 release, which is in preparation, = will also contain the new powerful ETS-NOCV = scheme: 

M. Mitoraj, A. Michalak and T. Ziegler, Chem. Theory Comput., 5 = (2009), 962

M. Mitoraj, A. Michalak and T. Ziegler, Organometallics, 28 = (2009), 3727

Best regards,
Stan van = Gisbergen 

On Aug 5, 2009, at = 10:52 AM, may abdelghani may01dz ~ yahoo.fr wrote:

Dear CCL's

How I can calculate the energies of chemical = bonds, in ADF

thank you = very much,


=

Dr. S.J.A. van = Gisbergen
Chief Executive = Officer
Scientific Computing & = Modelling NV
Theoretical Chemistry, Vrije = Universiteit
De Boelelaan 1083
1081 HV Amsterdam
The = Netherlands                 =                
T: +31-20-5987626    
F: +31-20-5987629



= --Apple-Mail-105-652326862-- From owner-chemistry@ccl.net Thu Aug 6 06:39:00 2009 From: "Sergio Emanuel Galembeck segalemb[A]usp.br" To: CCL Subject: CCL: How to calculate a bond energy Message-Id: <-39937-090805174219-6933-JpMPgdbZ2G8habh+z+wiIQ[#]server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 05 Aug 2009 17:41:57 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb^usp.br] Eduardo, Things are a little more complicated than your scheme, because there are large errors in the direct fragmentation of a chemical bond. To overcome this problem theoretical chemists have developed the isodesmic reactions, a reaction (actual or hypothetical) in which the types of bonds that are made in forming the products are the same as those which are broken in the reactants, according to IUPAC Gold Book: http://www.iupac.org/goldbook/I03272.pdf. There are some other types =20 of isodesmic reactions, as hodesmotic. If you need more information, please write to me. Best regards, Sergio Galembeck segalemb_at_usp.br Citando "Eduardo Lemos de Sa edulsa*o*quimica.ufpr.br" =20 : > > Sent to CCL by: "Eduardo Lemos de Sa" [edulsa#%#quimica.ufpr.br] > Sirs and Ladies > > I have a silly questions: how can I calculate a energy rising from a bond > between two atoms in a organic molecule? I guess that the answer can be: > calculate the SCF energy for the whole molecule, for two radicals > originated from the dissociation. Thus, bound energy would be: sum (SCF > energy for radicals) - SCF energy for the complete molecule. Am I right? > > Thank you in advance > > Yours > > Eduardo > > > > > > -- > Eduardo Lemos de Sa > edulsa*_*quimica.ufpr.br > Professor Assoc. II - Departamento de Quimica > Universidade Federal do Parana > C. P. 19081 > 81531-990 Curitiba/PR - Brazil > Fone (41) 3361 3300 > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > From owner-chemistry@ccl.net Thu Aug 6 07:12:01 2009 From: "Wendy Warr wendy##warr.com" To: CCL Subject: CCL: Report on ACS Meeting in Salt Lake City Message-Id: <-39938-090806065129-20673-DWCithSiZVkI/DHRifdtBg%x%server.ccl.net> X-Original-From: "Wendy Warr" Date: Thu, 6 Aug 2009 06:51:25 -0400 Sent to CCL by: "Wendy Warr" [wendy.:.warr.com] Chemical Information and Computation 2009, Number One; ACS National Meeting and Exposition, Salt Lake City, UT, March, 2009 Now going to press. Visit http://www.warr.com/ Cheminformatics, library design, fragment-based drug design, drug discovery, virtual screening, QSAR, pharmacophore elucidation, use of InChI, text mining, and more; plus news from more than 70 companies. New format, more detail, more graphics, more readable layout, greater value... Wendy Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./fax +44 (0)1477 533837 wendy|-|warr.com http://www.warr.com From owner-chemistry@ccl.net Thu Aug 6 09:08:01 2009 From: "Basma Ghazal basmaghazal+/-ymail.com" To: CCL Subject: CCL: Help Message-Id: <-39939-090806084059-17704-BSd8U1Mt5/y4jspX7c3bew,+,server.ccl.net> X-Original-From: Basma Ghazal Content-Type: multipart/alternative; boundary="0-280906288-1249559176=:67992" Date: Thu, 6 Aug 2009 04:46:16 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Basma Ghazal [basmaghazal]*[ymail.com] --0-280906288-1249559176=:67992 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear all, what=A0 free software is usually used for fixing protien?and What is the st= eps that i have to do for make the ligand attached to the residue? Regards,=0A=0A=0A --0-280906288-1249559176=:67992 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
D= ear all,

what&nb= sp; free software is usually used for fixing protien?and What is the steps = that i have to do for make the ligand attached to the residue?
Regards,

=0A=0A=0A=0A --0-280906288-1249559176=:67992-- From owner-chemistry@ccl.net Thu Aug 6 12:25:00 2009 From: "Matthew Clark mclark ~ pharmatrope.com" To: CCL Subject: CCL: free/open source docking programs Message-Id: <-39940-090806121334-13240-1uz/jOJurGVF/2q5chEdgQ##server.ccl.net> X-Original-From: Matthew Clark Content-Type: multipart/alternative; boundary="=-MGL0FEplejALZv1YPqmE" Date: Thu, 06 Aug 2009 11:40:44 -0400 Mime-Version: 1.0 Sent to CCL by: Matthew Clark [mclark.:.pharmatrope.com] --=-MGL0FEplejALZv1YPqmE Content-Type: text/plain Content-Transfer-Encoding: 7bit All, Is there a listing of free or open source molecular docking programs available somewhere? If you have experience with them, any opinion on which is the most reliable. I'm interested in the free open source ones, if any; I know about the commercial ones. Matthew Clark Pharmatrope Ltd. --=-MGL0FEplejALZv1YPqmE Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 7bit All,

Is there a listing of free or open source molecular docking programs available somewhere? 

If you have experience with them, any opinion on which is the most reliable. I'm interested in the free open source ones, if any; I know about the commercial ones.


Matthew Clark
Pharmatrope Ltd. --=-MGL0FEplejALZv1YPqmE-- From owner-chemistry@ccl.net Thu Aug 6 13:55:00 2009 From: "Ronald Salesky rsalesky++unm.edu" To: CCL Subject: CCL: free/open source docking programs Message-Id: <-39941-090806134815-14559-XpARDww3LCHSxvCrIscM0g[]server.ccl.net> X-Original-From: "Ronald Salesky" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain;charset=iso-8859-1;format="flowed" Date: Thu, 06 Aug 2009 11:17:56 -0600 MIME-Version: 1.0 Sent to CCL by: "Ronald Salesky" [rsalesky:_:unm.edu] Hi Matthew, There's autodock and mgltools from Scripps. http://autodock.scripps.edu/ http://mgltools.scripps.edu/ Best regards, Ron Salesky On Thu, 06 Aug 2009 11:40:44 -0400 "Matthew Clark mclark ~ pharmatrope.com"=20 wrote: > All, >=20 > Is there a listing of free or open source molecular=20 >docking programs > available somewhere? =20 >=20 > If you have experience with them, any opinion on which=20 >is the most > reliable. I'm interested in the free open source ones,=20 >if any; I know > about the commercial ones. >=20 >=20 > Matthew Clark > Pharmatrope Ltd. From owner-chemistry@ccl.net Thu Aug 6 15:00:01 2009 From: "Sudesh Kumari sudeshchem ~ gmail.com" To: CCL Subject: CCL:G: error while doing frequency calculation Message-Id: <-39942-090806130347-32615-i8B95ybVcWd4sX7+ogk/5w(-)server.ccl.net> X-Original-From: "Sudesh Kumari" Date: Thu, 6 Aug 2009 13:03:43 -0400 Sent to CCL by: "Sudesh Kumari" [sudeshchem[A]gmail.com] I am getting this EOF while reading ECP pointer card. Error termination via Lnk1e in /share/cluster/SLES9/ppc64/apps/gaussian/D.02/g03/l301.exe at Thu Aug 6 12:49:31 2009. My input file is %nprocshared=2 %mem=8GB %chk=Motol01f-0C2v.chk #b3lyp/gen pseudo=read Freq IOp(6/7=3, 7/33=1) #Geom=CheckPoint Guess=Read scf=symm Pop=Reg frequency 0 1 C H 0 6-311+G(d,p) ***** Mo 0 LanL2DZ ***** Mo 0 lanL2DZ I tried number of times but could not resolve it. Thank you for your help. From owner-chemistry@ccl.net Thu Aug 6 16:33:01 2009 From: "errol lewars elewars]![trentu.ca" To: CCL Subject: CCL: How to calculate a bond energy Message-Id: <-39943-090806162737-15168-JNfsBtS0GKXNRP8Fscb4Qg^^^server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 06 Aug 2009 15:31:41 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars=-=trentu.ca] 2009 Aug 06 Hello, The usual bond energies are 298 K enthalpy differences deltaH between fragments and reactants, e.g. C-C BE for CH3-CH3: deltaH(C-C) = 2H(CH3) - H(CH3CH3) This can be calculated directly, if your molecule is not too big (see below) by a high-accuracy multistep method. I give a few examples. A CBS-4M CH3 CBS-4 Enthalpy= -39.756477, CH3-CH3 CBS-4 Enthalpy= -79.658510 deltaH = 2 H(CH3) - H(CH3CH3) = 2(-39.756477) - (-79.658510) = 0.145556 = 382.2 kJ mol-1 B G3MP2 CH3 G3MP2 Enthalpy= -39.752870, CH3-CH3 G3MP2 Enthalpy= -79.646717 deltaH = 2 H(CH3) - H(CH3CH3) = 2(-39.752870) - (-79.646717) = 0.140977 = 370.2 kJ mol-1 C CBS-QB3 CH3 CBS-QB3 Enthalpy= -39.740778, CH3-CH3 CBS-QB3 Enthalpy= -79.626122 deltaH = 2 H(CH3) - H(CH3CH3) = 2(-39.740778) - (-79.626122) = 0.144566 = 379.6 kJ mol-1 D CBS-APNO CH3 CBS-APNO Enthalpy= -39.740778, CH3-CH3 CBS-APNO Enthalpy= -79.626122 deltaH = 2 H(CH3) - H(CH3CH3) = 2(-39.799535) - (-79.743561) = 0.144491 = 379.4 kJ mol-1 I convertes hartree to JkJ mol-1 by mult by 2626 (as if 2625.5 makes any difference). The exp C-C bond enthalpy for CH3CH3 is said to be 377.0 kJ mol-1 (90.1 kcal mol-1; E. V. Anslyn, D. A. Dougherty, "Modern Physical Organic Chemisty", University Science Books, Sausalito, CA, 2006; p 72. The CBS-APNO value may be better than the exp. CBS-4M is the least, CBS-APNO the most, accurate; G3MP2 and CBS-QB3 are comparable. The approximate size limits and times for these methods are (number of heavy atoms/hours for that number): CBS-4m, 19/3h; G3MP2, 13/12h; CBS-QB3, 10/9h; CBS-APNO, 5/2.4 Using energies at the SCF (Hartreee-Fock) level your bond E will not be good; even DFT or MP2 will probably be significantly inferior to these methods. If your molecule is too big for a high-accuracy multistep method, you could use an isodesmic reaction incorporated into a thermodynamic cycle. You can check these methods in a book on computational chemistry. Good luck. E. Lewars === Eduardo Lemos de Sa edulsa*o*quimica.ufpr.br wrote: > Sent to CCL by: "Eduardo Lemos de Sa" [edulsa#%#quimica.ufpr.br] > Sirs and Ladies > > I have a silly questions: how can I calculate a energy rising from a bond > between two atoms in a organic molecule? I guess that the answer can be: > calculate the SCF energy for the whole molecule, for two radicals > originated from the dissociation. Thus, bound energy would be: sum (SCF > energy for radicals) - SCF energy for the complete molecule. Am I right? > > Thank you in advance > > Yours > > Eduardo > > > > > > From owner-chemistry@ccl.net Thu Aug 6 17:07:01 2009 From: "jean-francois prieur jfprieur|,|gmail.com" To: CCL Subject: CCL: free/open source docking programs Message-Id: <-39944-090806134036-13971-XnHnDmaKnB/kXR+85E3e3w : server.ccl.net> X-Original-From: jean-francois prieur Content-Type: multipart/alternative; boundary=000e0cd6b29a2c35c704707c8a45 Date: Thu, 6 Aug 2009 17:35:03 +0000 MIME-Version: 1.0 Sent to CCL by: jean-francois prieur [jfprieur[-]gmail.com] --000e0cd6b29a2c35c704707c8a45 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit This software, FORECASTER, includes a docking program called FITTED. http://www.fitted.ca/ I believe that they are still distributing FITTED free of charge http://fitted.ca/index.php?option=com_content&task=view&id=18&Itemid=36 Regards, JF Prieur PS. I am not affiliated with the research group above. 2009/8/6 Matthew Clark mclark ~ pharmatrope.com > All, > > Is there a listing of free or open source molecular docking programs > available somewhere? > > If you have experience with them, any opinion on which is the most > reliable. I'm interested in the free open source ones, if any; I know about > the commercial ones. > > > Matthew Clark > Pharmatrope Ltd. > --000e0cd6b29a2c35c704707c8a45 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable This software, FORECASTER, includes a docking program called FITTED.
http://www.fitted.ca/

I believe that they are still distributing FITTED fr= ee of charge

=

Regards,
JF Prieur

PS. I am not aff= iliated with the research group above.

20= 09/8/6 Matthew Clark mclark ~ pharmatrop= e.com <= owner-chemistry##ccl.net>
=20 =20
All,

Is there a listing of free or open source molecular docking programs availa= ble somewhere?=A0

If you have experience with them, any opinion on which is the most reliable= . I'm interested in the free open source ones, if any; I know about the= commercial ones.


Matthew Clark
Pharmatrope Ltd.

--000e0cd6b29a2c35c704707c8a45-- From owner-chemistry@ccl.net Thu Aug 6 18:05:00 2009 From: "=?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= jgcj-,-fct.unl.pt" To: CCL Subject: CCL: protein-small molecules reactions Message-Id: <-39945-090806175149-1874-cj9X1MRkMVAZGFxIFBODbw(_)server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= Content-Type: multipart/alternative; boundary=001636c5a758aa3a9804707fb5a1 Date: Thu, 6 Aug 2009 22:21:57 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= [jgcj{=}fct.unl.pt] --001636c5a758aa3a9804707fb5a1 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable dear all, i'm studying the reaction between a protein and a small molecule. from experiments we know it forms covalent adducts to four residues, which have been clearly identified. my question is: how can i predict, from the structures of both the protein and the molecule, which are the residues most likely to react? i was planning to get a solvent accessibility map of the protein and then "react" the molecule to those residues (we know it's an sn2 reaction), but = i can't figure out what approach to use to model those reactions using the **whole protein**. any comments will be very much appreciated! cheers, g. --=20 Gon=E7alo Justino, Ph.D. ---------------------------------------------------- [Computational & Radical BioChemistry] Requimte/CQFB - Department of Chemistry Faculty of Sciences and Technology New University of Lisbon 2829-516 Caparica Portugal Phone: (+351) 212 948 300 ext. 10971 Fax: (+351) 212 948 550 ---------------------------------------------------- All saints have a past, all sinners have a future. --001636c5a758aa3a9804707fb5a1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable dear all,

i'm studying the reaction between a protein and a smal= l molecule. from experiments we know it forms covalent adducts to four resi= dues, which have been clearly identified.

my question is: how can i = predict, from the structures of both the protein and the molecule, which ar= e the residues most likely to react?

i was planning to get a solvent accessibility map of the protein and th= en "react" the molecule to those residues (we know it's an sn= 2 reaction), but i can't figure out what approach to use to model those= reactions using the **whole protein**.

any comments will be very much appreciated!

cheers,
g.


--
Gon=E7alo Justino, Ph.D.
-----------------= -----------------------------------
[Computational & Radical BioChem= istry]
Requimte/CQFB - Department of Chemistry
Faculty of Sciences and Technolo= gy
New University of Lisbon
2829-516 Caparica
Portugal
Phone: (= +351) 212 948 300 ext. 10971
Fax: (+351) 212 948 550
----------------= ------------------------------------
All saints have a past, all sinners have a future.
--001636c5a758aa3a9804707fb5a1-- From owner-chemistry@ccl.net Thu Aug 6 21:01:01 2009 From: "David Gallagher gallagher.da#gmail.com" To: CCL Subject: CCL: protein-small molecules reactions Message-Id: <-39946-090806205524-31115-8xDxRoGyW0w/X640XGEUow^server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary=002215048e3b2381440470829d65 Date: Thu, 6 Aug 2009 17:49:51 -0700 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da%gmail.com] --002215048e3b2381440470829d65 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Gon=E7alo, Modelling reactions (making and breaking of bonds) requires a quantum metho= d and is rarely quick and easy, particularly with large systems, but here is = a suggested strategy: General points: 1. Most quantum methods scale in time and memory-use by the cube of the number of atoms, or worse. So, start by modelling the smallest representative part of your system to check that everything works as expected, before scaling up to model the full system. For example, use jus= t the reacting atoms and the next 2 or 3 atoms connected to them (you may nee= d lock some atoms and to terminate some atoms with hydrogens). This can save a lot of time in the long run, particularly when trying to model transition states. 2. Start by using the fastest quantum method available to you to test that the optimizations work correctly, before trying higher level methods which can be dramatically slower. I would recommend starting with MOPAC2009 for four reasons, 1) it is one of the fastest quantum methods available, 2) it can model reactions on systems of up to 15,000 atoms (using a linear scalin= g algorithm), 3) PM6 parameterization in MOPAC2009 includes heats of formation of biological molecules, 4) it is free to academics. The download link is at http://cacheresearch.com/mopac.html#mopac-sales 3. Although, for speed, you may want to start by testing simple gas phase calculations, a water solvent field (e.g. COSMO), or explicit waters should be included for biological systems. Also, you should check that the protein protonation states are correctly assigned (MOPAC2009 does some automatic checking). Thermodynamics: If the reactions are reversible and in equilibrium, then a simple compariso= n of the free energies of the reactants and all possible adducts may be sufficient to predict the main product (largest drop in delta-G). Kinetics: If reactions rates are important, then you would need to model the transition state(s) for each reaction and determine the activation energies= . Although most quantum methods can get the relative order correct, they typically overestimate the activation energies, so calibration may be needed. A guide, "Strategies for finding transition states", is posted at http://cacheresearch.com/presentations.html . Hope this helps, David Gallagher CACheResearch.com 2009/8/6 Gon=E7alo C. Justino jgcj-,-fct.unl.pt > dear all, > > i'm studying the reaction between a protein and a small molecule. from > experiments we know it forms covalent adducts to four residues, which hav= e > been clearly identified. > > my question is: how can i predict, from the structures of both the protei= n > and the molecule, which are the residues most likely to react? > > i was planning to get a solvent accessibility map of the protein and then > "react" the molecule to those residues (we know it's an sn2 reaction), bu= t i > can't figure out what approach to use to model those reactions using the > **whole protein**. > > any comments will be very much appreciated! > > cheers, > g. > > > > -- > Gon=E7alo Justino, Ph.D. > ---------------------------------------------------- > [Computational & Radical BioChemistry] > Requimte/CQFB - Department of Chemistry > Faculty of Sciences and Technology > New University of Lisbon > 2829-516 Caparica > Portugal > Phone: (+351) 212 948 300 ext. 10971 > Fax: (+351) 212 948 550 > ---------------------------------------------------- > All saints have a past, all sinners have a future. > --002215048e3b2381440470829d65 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi=A0Gon=E7alo,

Modelling reactions (making and breaking= of bonds) requires a quantum method and is rarely quick and easy, particul= arly with large systems, but here is a suggested strategy:

General points:
1. Most quantum methods scale in time and me= mory-use by the cube of the number of atoms, or worse. =A0So, start by mode= lling the smallest representative part of your system to check that everyth= ing works as expected, before scaling up to model the full system. =A0For e= xample, use just the reacting atoms and the next 2 or 3 atoms connected to = them (you may need lock some atoms and to terminate some atoms with hydroge= ns). =A0This can save a lot of time in the long run, particularly when tryi= ng to model transition states.

2. Start by using the fastest quantum method available = to you to test that the optimizations work correctly, before trying higher = level methods which can be dramatically slower. =A0I would recommend starti= ng with MOPAC2009 for four reasons, 1) it is one of the fastest quantum met= hods available, =A02) it can model reactions on systems of up to 15,000 ato= ms (using a linear scaling algorithm), =A03) PM6=A0parameterization=A0in MO= PAC2009 includes heats of formation of biological molecules, =A04) it is fr= ee to academics. =A0The download link is at=A0http://cacheresearch.com/mopac.html#mopac-sa= les

3. =A0Although, for speed, you may want to start by tes= ting simple gas phase calculations, a water solvent field (e.g. COSMO), or = explicit waters should be included for biological systems. Also, you should= check that the protein protonation states are correctly assigned (MOPAC200= 9 does some automatic checking).

Thermodynamics:
If the reactions are reversib= le and in equilibrium, then a simple comparison of the free energies of the= reactants and all possible adducts may be sufficient to predict the main p= roduct (largest drop in delta-G).

Kinetics:
If reactions rates are important, t= hen you would need to model the transition state(s) for each reaction and d= etermine the activation energies. =A0Although most quantum methods can get = the relative order correct, they typically overestimate the activation ener= gies, so calibration may be needed. =A0A guide, "Strategies for finding transitio= n states",=A0is posted at=A0http://cacheresearch.com/presentations.html=A0.

Hope this helps,
David Gallagher
CA= CheResearch.com


2009/8/6 Gon=E7alo C. Justino jgcj-,-= fct.unl.pt <owner-chemistry a ccl.net>
dear all,

i'm studying the react= ion between a protein and a small molecule. from experiments we know it for= ms covalent adducts to four residues, which have been clearly identified.
my question is: how can i predict, from the structures of both the prot= ein and the molecule, which are the residues most likely to react?

i was planning to get a solvent accessibility map of the protein and th= en "react" the molecule to those residues (we know it's an sn= 2 reaction), but i can't figure out what approach to use to model those= reactions using the **whole protein**.

any comments will be very much appreciated!

cheers,
g.


--
Gon=E7alo Justino, Ph.D.
-----------------= -----------------------------------
[Computational & Radical BioChem= istry]
Requimte/CQFB - Department of Chemistry
Faculty of Sciences and Technolo= gy
New University of Lisbon
2829-516 Caparica
Portugal
Phone: (= +351) 212 948 300 ext. 10971
Fax: (+351) 212 948 550
----------------= ------------------------------------
All saints have a past, all sinners have a future.

--002215048e3b2381440470829d65-- From owner-chemistry@ccl.net Thu Aug 6 21:36:01 2009 From: "Gennady L. Gutsev gennady.gutsev{:}famu.edu" To: CCL Subject: CCL:G: error while doing frequency calculation Message-Id: <-39947-090806211543-5446-l3qT1mT3l0zAqT4B8+J9Pw]![server.ccl.net> X-Original-From: "Gennady L. Gutsev" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CA16FD.B341F0F8" Date: Thu, 6 Aug 2009 21:23:42 -0400 MIME-Version: 1.0 Sent to CCL by: "Gennady L. Gutsev" [gennady.gutsev^-^famu.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01CA16FD.B341F0F8 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Sudesh, I guess you need to delete "pseudo=3Dread"=20 and=20 "Mo 0 lanL2DZ" However, than I am puzzled how you was able to get converged geometry with this deck. =20 Another option: replace "gen pseudo=3Dread" with "chkbasis" -----Original Message----- > From: owner-chemistry+gennady.gutsev=3D=3Dfamu.edu##ccl.net on behalf of = Sudesh Kumari sudeshchem ~ gmail.com Sent: Thu 8/6/2009 1:03 PM To: Gennady L. Gutsev Subject: CCL:G: error while doing frequency calculation =20 Sent to CCL by: "Sudesh Kumari" [sudeshchem[A]gmail.com] I am getting this EOF while reading ECP pointer card. Error termination via Lnk1e in = /share/cluster/SLES9/ppc64/apps/gaussian/D.02/g03/l301.exe at Thu Aug 6 = 12:49:31 2009. My input file is=20 %nprocshared=3D2 %mem=3D8GB %chk=3DMotol01f-0C2v.chk #b3lyp/gen pseudo=3Dread Freq IOp(6/7=3D3, 7/33=3D1) #Geom=3DCheckPoint Guess=3DRead scf=3Dsymm Pop=3DReg frequency 0 1 C H 0 6-311+G(d,p) ***** Mo 0 LanL2DZ ***** Mo 0 lanL2DZ I tried number of times but could not resolve it. Thank you for your help. -=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------_=_NextPart_001_01CA16FD.B341F0F8-- From owner-chemistry@ccl.net Thu Aug 6 22:16:01 2009 From: "Carlos F. Lagos carlos-#-cbuc.cl" To: CCL Subject: CCL: free/open source docking programs Message-Id: <-39948-090806221136-11447-nC8RKYtx9ICNXlACTCtozA^server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0026_01CA16DD.CA9B7690" Date: Thu, 6 Aug 2009 21:35:17 -0400 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [carlos() cbuc.cl] This is a multi-part message in MIME format. ------=_NextPart_000_0026_01CA16DD.CA9B7690 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit A list of some available for academics e-Hits http://www.simbiosys.ca/ehits/index.html DOCK http://dock.compbio.ucsf.e du/ AutoDock http://autodock.scripps.ed u/ VINA http://vina.scripps.edu/ GEMDOCK http://gemdock.life.nctu.e du.tw/dock/ Discovery Studio 2.5 (30 days free trial), CDocker, Libdock & LigandFit http://accelrys.com/products/discovery-studio/ Molegro Virtual Docker (30 days free trial) http://www.molegro.com/mvd-product.php ArgusLab http://www.arguslab.com/ Rosetta http://www.rosettacommons.org/software/index.html DockVision http://dockvision.com/ FRED http://www.eyesopen.com/products/applications/fred.html PLANTS http://www.tcd.uni-konstanz.de/research/plants.php QF Carlos F. Lagos Centre for Bioinformatics CBUC, Faculty of Biological Sciences Medicinal Chemistry Laboratory MCL, Faculty of Chemistry P. Universidad Catolica de Chile Portugal 49, Zocalo I 6513492 Santiago-Chile Phone: +56 2 3541911 I http://www.cbuc.cl _____ De: owner-chemistry+carlos==cbuc.cl]_[ccl.net [mailto:owner-chemistry+carlos==cbuc.cl]_[ccl.net] En nombre de Matthew Clark mclark ~ pharmatrope.com Enviado el: Jueves, 06 de Agosto de 2009 11:41 Para: Lagos, Carlos F Asunto: CCL: free/open source docking programs All, Is there a listing of free or open source molecular docking programs available somewhere? If you have experience with them, any opinion on which is the most reliable. I'm interested in the free open source ones, if any; I know about the commercial ones. Matthew Clark Pharmatrope Ltd. __________ Information from ESET NOD32 Antivirus, version of virus signature database 4306 (20090804) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com ------=_NextPart_000_0026_01CA16DD.CA9B7690 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

A list = of some available for academics

 

e-Hits=

http://www.simbiosys.ca= /ehits/index.html

 =

DOCK
http://dock.compbio.ucsf.edu/

 

AutoDock
http://autodock.scripps.edu/

VINA
http://vina.scripps.edu/

GEMDOCK
http://gemdock.life.nctu.edu.tw/dock/<= /font>

 

Discovery= Studio 2.5 (30 days free trial), CDocker, Libdock & = LigandFit

http://accelrys.c= om/products/discovery-studio/

 

Molegro = Virtual Docker (30 days free trial)

http://www.molegro.com/mv= d-product.php

 

ArgusLab<= o:p>

http://www.arguslab.com/=

 

Rosetta

http://www.ros= ettacommons.org/software/index.html

 

DockVision=

http://dockvision.com/

 

FRED

http://w= ww.eyesopen.com/products/applications/fred.html

 

PLANTS=

http://www.tc= d.uni-konstanz.de/research/plants.php

 

 

QF = Carlos F. Lagos
Centre for Bioinformatics CBUC, Faculty of Biological = Sciences

Medicinal = Chemistry Laboratory MCL, Faculty of Chemistry
P. Universidad Catolica de Chile
Portugal 49, Zocalo I 6513492 Santiago-Chile
Phone: +56 2 3541911 I http://www.cbuc.cl

 

De: owner-chemistry+carlos=3D=3Dcbuc.cl]_[ccl.net = [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl]_[ccl.net] En nombre de Matthew = Clark mclark ~ pharmatrope.com
Enviado el: Jueves, 06 de = Agosto de 2009 11:41
Para: Lagos, Carlos F =
Asunto: CCL: free/open = source docking programs

 

All,

Is there a listing of free or open source molecular docking programs = available somewhere? 

If you have experience with them, any opinion on which is the most = reliable. I'm interested in the free open source ones, if any; I know about the commercial ones.


Matthew Clark
Pharmatrope Ltd.

__________ Information from ESET NOD32 Antivirus, version of virus = signature database 4306 (20090804) __________

The message was checked by ESET NOD32 Antivirus.

http://www.eset.com

------=_NextPart_000_0026_01CA16DD.CA9B7690-- From owner-chemistry@ccl.net Thu Aug 6 23:17:00 2009 From: "Venable, Richard (NIH/NHLBI) E venabler+/-nhlbi.nih.gov" To: CCL Subject: CCL:G: protein-small molecules reactions Message-Id: <-39949-090806221305-12105-rBOA9gHi1Cm6lbpm2wlSjQ#%#server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 6 Aug 2009 21:40:31 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler : nhlbi.nih.gov] There are a number of programs and approaches to combined QM/MM calculation= s. I am aware that CHARMM has a number of interfaces to QM programs; the b= est two (IMHO) interfaces are with Q-Chem and GAMESS-UK, in part because bo= th allow the use of a gaussian distribution to represent the MM charges in = the QM part. None of these are free programs, but the costs are modest for academic styl= e research groups in most cases. -- Rick Venable 5635FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 8/6/09 5:21 PM, "Gon=E7alo C. Justino jgcj-,-fct.unl.pt" wrote: dear all, i'm studying the reaction between a protein and a small molecule. from expe= riments we know it forms covalent adducts to four residues, which have been= clearly identified. my question is: how can i predict, from the structures of both the protein = and the molecule, which are the residues most likely to react? i was planning to get a solvent accessibility map of the protein and then "= react" the molecule to those residues (we know it's an sn2 reaction), but i= can't figure out what approach to use to model those reactions using the *= *whole protein**. any comments will be very much appreciated! cheers, g.