From owner-chemistry@ccl.net Wed Aug 4 01:14:00 2010 From: "Peter Khlyabich khlyabic*usc.edu" To: CCL Subject: CCL:G: TDDFT excitation coefficient Message-Id: <-42422-100804011328-15570-K2SIUHMYfUainovWkMegDg ~ server.ccl.net> X-Original-From: "Peter Khlyabich" Date: Wed, 4 Aug 2010 01:13:27 -0400 Sent to CCL by: "Peter Khlyabich" [khlyabic:_:usc.edu] Dear Colleagues, I'm running TDDFT calculations using Gaussian 03. In the output file I get the following: Excited State 4: Singlet-A 2.2578 eV 549.15 nm f=0.0518 495 -> 499 -0.13275 496 -> 498 0.60862 496 -> 500 0.14546 497 -> 499 -0.25852 I understand that 2.2578 eV is the excitation energy. f=0.0518 is oscillator strength (proportional to the intensity of excitation). 495->499 are orbitals excited from and to. -0.13275 is the coefficient of the wavefunction for each excitation. My question is: Why this excitation coefficient is negative? When I calculate the excitation probability is the probability of excitation from 495 to 499 3.52% or -3.52%? In some papers I saw negative excitation probability. What does it mean? Sincerely, Peter Khlyabich ----------------------------------------------------- University of Southern California Chemistry Department Prof. Barry C. Thompson Group phone: 213-740-2599 e-mail: khlyabic,,usc.edu From owner-chemistry@ccl.net Wed Aug 4 02:05:01 2010 From: "Visvaldas K. coyote_v2002 * yahoo.com" To: CCL Subject: CCL: charmm energy Message-Id: <-42423-100804013633-22265-zAdjEACBTo0V+PcSlIc/vw ~~ server.ccl.net> X-Original-From: "Visvaldas K." Content-Type: multipart/alternative; boundary="0-141650032-1280900184=:63621" Date: Tue, 3 Aug 2010 22:36:24 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Visvaldas K." [coyote_v2002]|[yahoo.com] --0-141650032-1280900184=:63621 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable I am not sure if this is of much help, but I couldn't help noticing that th= e calculations are done using perl script, so by analyzing what commands or= components are activated when using different flags you could try to figur= e out the reasons for the discrepancy yourself. Sorry I can't help more her= e much since we don't have CHARMM. Vis Kairys =0A> =0A> Sent to CCL by: "Tatsiana =C2=A0Kirys" [tatsiana%x%ku.edu] =0A> Hi all, =0A> =0A> i calculate protein energy using enrCHARMM.pl script. i run it with gb= and without for the same protein file. =0A> =0A> enerCHARMM.pl -out total -log file.log file.pdb =0A> BONDs =C2=A0 =C2=A0 =C2=A0 =C2=A092.56954 =0A> ANGLes =C2=A0 =C2=A0 =C2=A0336.00337 =0A> UREY-b =C2=A0 =C2=A0 =C2=A0 24.08096 =0A> DIHEdrals =C2=A0 604.46805 =0A> CMAPs =C2=A0 =C2=A0 =C2=A0-134.62511 =0A> VDWaals =C2=A0 =C2=A0-476.01682 =0A> ELEC =C2=A0 =C2=A0 =C2=A0-2041.80015 =0A> =0A> =0A> enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb =0A> =0A> BONDs =C2=A0 =C2=A0 =C2=A0 =C2=A092.56954 =0A> ANGLes =C2=A0 =C2=A0 =C2=A0336.00337 =0A> UREY-b =C2=A0 =C2=A0 =C2=A0 24.08096 =0A> DIHEdrals =C2=A0 604.46805 =0A> CMAPs =C2=A0 =C2=A0 =C2=A0-134.62511 =0A> VDWaals =C2=A0 =C2=A0-485.01639 =0A> ELEC =C2=A0 =C2=A0 =C2=A0-2021.31359 =0A> ASP =C2=A0 =C2=A0 =C2=A0 =C2=A0 102.42587 =0A> GBEnr =C2=A0 =C2=A0 -1479.15727 =0A> =0A> i dont understand why Electrostatic and VdW energy terms are different= . Any help will be very appreciated!!!=D0=AF =D0=B2 =D0=9C=D0=BE=D0=B5=D0= =BC =D0=9C=D0=B8=D1=80=D0=B5 - http://my.mail.ru/mail/nushki/ =0A=0A =0A =0A =0A-=3D This is automatically added to each message by the mailing script = =3D- =0A =0AE-mail to subscribers: CHEMISTRY(!)ccl.net or use: =0A =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0AE-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net or use =0A =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0A=0A =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/chemistry/sub_unsub.shtml =0A =0A=0A =0A=0A=0A =0A=0A =0A =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt =0A =0A=0A =0A =0A --=20 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Mahmoud A. A= . Ibrahim=C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=20 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0=C2=A0 Current Address =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 7.05, School = of Chemistry, =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 The University of Manchest= er, =0A=C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 Oxford Road, Manchester, M13 9PL,=20 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0=C2=A0 United Kingdom. =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 Home Address =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Chemistry De= partment, =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0= Faculty of Science, =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 Minia University, =0A=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0=C2=A0 Minia 61519, =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Egypt.=20 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0= Contact Information =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 Email: m.ibrahim(!)compchem.net =0A=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Website: www.compchem.n= et =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 Fax No= .: +20862342601 =0A=0A=0A=0A=0A --0-141650032-1280900184=:63621 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
I am not sure if this is of much help, but I = couldn't help noticing that the calculations are done using perl script, so= by analyzing what commands or components are activated when using differen= t flags you could try to figure out the reasons for the discrepancy yoursel= f. Sorry I can't help more here much since we don't have CHARMM.
Vis Kai= rys
=0A>
=0A> Sent to CCL by: "Tatsiana &nbs= p;Kirys" [tatsiana%x%ku.edu]
=0A> Hi all,
=0A>
=0A> i calculate pro= tein energy using enrCHARMM.pl script. i run it with gb and without for the= same protein file.
=0A>
=0A> enerCHARMM.pl -out total -log fil= e.log file.pdb
=0A> BONDs        92.56954
=0A&= gt; ANGLes      336.00337
=0A> UREY-b     &n= bsp; 24.08096
=0A> DIHEdrals   604.46805
=0A> CMAPs  =    -134.62511
=0A> VDWaals    -476.01682
=0A&= gt; ELEC      -2041.80015
=0A>
=0A>
=0A> e= nerCHARMM.pl -out total -par gb -log file_gb.log file.pdb
=0A>
=0A= > BONDs        92.56954
=0A> ANGLes   &nb= sp;  336.00337
=0A> UREY-b       24.08096
=0A&= gt; DIHEdrals   604.46805
=0A> CMAPs      -134.62= 511
=0A> VDWaals    -485.01639
=0A> ELEC    = ;  -2021.31359
=0A> ASP         102.42587=0A> GBEnr     -1479.15727
=0A>
=0A> i dont under= stand why Electrostatic and VdW energy terms are different. Any help will b= e very appreciated!!!=D0=AF =D0=B2 =D0=9C=D0=BE=D0=B5=D0=BC =D0=9C=D0=B8=D1= =80=D0=B5 - http://my.mail.ru/mail/nushki/
=0A=0A
=0A
=0A=0A-=3D This is automatically added to each message by the mailing script= =3D-
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--
      &nb= sp;           Mahmoud A. A. Ibrahim    &= nbsp;   
              &nb= sp;        Current Address
      &nbs= p;          7.05, School of Chemistry,
  &= nbsp;           The University of Manchester,
= =0A         Oxford Road, Manchester, M13 9PL,
=                      = ;  United Kingdom.

            &n= bsp;           Home Address
     = ;             Chemistry Department,
 =                    Facul= ty of Science,
                &= nbsp;       Minia University,
=0A      &nb= sp;                    Mi= nia 61519,
                 = ;               Egypt.

  &n= bsp;                  Contact = Information
           Email: m.ibrahim(!)compchem.n= et
=0A              Website: www.comp= chem.net
                &nb= sp;  Fax No.: +20862342601
=0A
=0A

=0A=0A=0A=0A=0A=0A=0A=0A= --0-141650032-1280900184=:63621-- From owner-chemistry@ccl.net Wed Aug 4 03:59:00 2010 From: "may abdelghani may01dz===yahoo.fr" To: CCL Subject: CCL: Ruthenium force field parameter Message-Id: <-42424-100804035154-1391-h65nYlogQQrtNsJG9qauQg*o*server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-1402741889-1280908307=:47270" Date: Wed, 4 Aug 2010 07:51:47 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz : yahoo.fr] --0-1402741889-1280908307=:47270 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CLLers, There is a Ruthenium=0Aforce field parameter ??? =A0 may abdelghani=09Laboratoire de chimie des mat=E9riaux et des vivants: Acti= vit=E9, R=E9activit=E9=0A=0A=0A --0-1402741889-1280908307=:47270 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear CLLers,


There is a Ruthenium=0Aforce field parameter= ??? =A0


may abdelghani=09
<= div style=3D"">Laboratoire de chimie des m= at=E9riaux et des vivants: Activit=E9, R=E9activit=E9<= /font>

=0A=0A=0A=0A=0A --0-1402741889-1280908307=:47270-- From owner-chemistry@ccl.net Wed Aug 4 05:10:00 2010 From: "Gkourmpis, Thomas Thomas.Gkourmpis/a\borealisgroup.com" To: CCL Subject: CCL: Ruthenium force field parameter Message-Id: <-42425-100804050900-21586-bvUGZXQ54wNX6W7bCBH09w],[server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_2BD27C21A5B53C4AB53F403FC915A1820145C9E1D2CMS02mignetwo_" Date: Wed, 4 Aug 2010 11:08:48 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis[A]borealisgroup.com] --_000_2BD27C21A5B53C4AB53F403FC915A1820145C9E1D2CMS02mignetwo_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable You need to be a bit more specific on the question you ask=2E What sort of = Force Field parameters are you looking for and for what purpose (Molecular = Dynamics or something else?)=2E In the literature there are a lot of parame= ters and IR/NMR data for Ruthenium based compounds and I know that MM3 Forc= e Field has some Ruthenium parameters, but I don't know how good they are o= r if they're of any use to you=2E=0D=0ACheck out this reference for the MM3= case (I'm sure it is not the only one) Inorg=2E Chem=2E, 1998, 37 (16), pp= 4120-4127=0D=0A=0D=0AI've never used Ruthenium myself so I might be wrong = here=2E If that's the case I do apologise in advance=2E=0D=0A=0D=0AI hope t= his helps=0D=0A=0D=0AThomas=0D=0A=0D=0AFrom: owner-chemistry+thomas=2Egkour= mpis=3D=3Dborealisgroup=2Ecom(~)ccl=2Enet [mailto:owner-chemistry+thomas=2Egk= ourmpis=3D=3Dborealisgroup=2Ecom(~)ccl=2Enet] On Behalf Of may abdelghani may= 01dz=3D=3D=3Dyahoo=2Efr=0D=0ASent: Wednesday, August 04, 2010 9:52 AM=0D=0A= To: Gkourmpis, Thomas=0D=0ASubject: CCL: Ruthenium force field parameter=0D= =0A=0D=0ADear CLLers,=0D=0A=0D=0AThere is a Ruthenium force field parameter= ???=0D=0A=0D=0Amay abdelghani=0D=0ALaboratoire de chimie des mat=E9riaux e= t des vivants: Activit=E9, R=E9activit=E9=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A --_000_2BD27C21A5B53C4AB53F403FC915A1820145C9E1D2CMS02mignetwo_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =0D=0A=0D=0A=0D=0A=0D=0A=0D=0A<= style>=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A
=0D=0A=0D=0A

Y= ou=0D=0Aneed to be a bit more specific on the question you ask=2E What sort= of Force=0D=0AField parameters are you looking for and for what purpose (M= olecular Dynamics=0D=0Aor something else?)=2E In the literature there are a= lot of parameters and IR/NMR=0D=0Adata for Ruthenium based compounds and I= know that MM3 Force Field has some=0D=0ARuthenium parameters, but I don= 217;t know how good they are or if they’re=0D=0Aof any use to you=2E =

=0D=0A=0D=0A

Check=0D=0Aout this referen= ce for the MM3 case (I’m sure it is not the only one) Inorg=2E Chem=2E, 1998, 37 (16), pp=0D=0A4120–4127

=0D=0A=0D= =0A

 

=0D=0A=0D=0A

I= 217;ve=0D=0Anever used Ruthenium myself so I might be wrong here=2E If that= ’s the case=0D=0AI do apologise in advance=2E

= =0D=0A=0D=0A

 

=0D=0A=0D=0A

I=0D=0Ahope this helps

=0D=0A=0D=0A

 

=0D=0A=0D=0A

Thomas<= /span>

=0D=0A=0D=0A

 

=0D=0A=0D=0A
=0D=0A=0D=0A

From:=0D=0Aowner-chemistry+thomas=2Egko= urmpis=3D=3Dborealisgroup=2Ecom(~)ccl=2Enet=0D=0A[mailto:owner-chemistry+thom= as=2Egkourmpis=3D=3Dborealisgroup=2Ecom(~)ccl=2Enet] On=0D=0ABehalf Of may abdelghani may01dz=3D=3D=3Dyahoo=2Efr
=0D=0ASent: Wednesday,= August 04, 2010 9:52 AM
=0D=0ATo: Gkourmpis, Thomas
=0D=0A= Subject: CCL: Ruthenium force field parameter

=0D= =0A=0D=0A
=0D=0A=0D=0A

 

=0D=0A= =0D=0A=0D=0A =0D=0A =0D=0A =0D=0A
= =0D=0A

Dear=0D=0A CLLers,

=0D=0A

 =

=0D=0A

There is a Ruthenium force field parameter=0D=0A ???  <= /o:p>

=0D=0A

 

=0D=0A
=0D= =0A

may abdelghani=A0=A0=A0=A0=A0= =A0=A0

=0D=0A
=0D=0A
=0D= =0A

Laboratoire = de chimie des mat=E9riaux et=0D=0A des vivants: Activit=E9, R=E9activit=E9=

=0D=0A
=0D=0A
=0D=0A=0D=0A

 

=0D= =0A=0D=0A
=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A --_000_2BD27C21A5B53C4AB53F403FC915A1820145C9E1D2CMS02mignetwo_-- From owner-chemistry@ccl.net Wed Aug 4 07:32:00 2010 From: "Anton Nizovtsev nanto*_*mail.ru" To: CCL Subject: CCL: O2 (1sigma+g) Message-Id: <-42426-100804073001-22318-cR15Ew3vlUy1Ij69p0eJug ~ server.ccl.net> X-Original-From: "Anton Nizovtsev" Date: Wed, 4 Aug 2010 07:30:00 -0400 Sent to CCL by: "Anton Nizovtsev" [nanto^mail.ru] Dear CCL members, Is it correct to say that the 1sigma+g state of molecular oxygen is considered if the restricted single-reference methods (RDFT, RMPn, RCCSD etc) are used? Which methods (if it possible) can be used for this task besides multireference ones? Thanks in advance, Anton From owner-chemistry@ccl.net Wed Aug 4 08:06:00 2010 From: "John McKelvey jmmckel^_^gmail.com" To: CCL Subject: CCL:G: TDDFT excitation coefficient Message-Id: <-42427-100804075042-27860-iuDx584H1PjfQPE3ZDf2wA%server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 4 Aug 2010 07:50:34 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel%x%gmail.com] As in most diagonalization procedures over an implicit/explicit orthogonal space it is the square of the coefficients that is the weight, with the sum of squares over all coefficients being 1. John McKelvey On Wed, Aug 4, 2010 at 1:13 AM, Peter Khlyabich khlyabic*usc.edu wrote: > > Sent to CCL by: "Peter  Khlyabich" [khlyabic:_:usc.edu] > Dear Colleagues, > > I'm running TDDFT calculations using Gaussian 03. In the output file I get the following: > >  Excited State   4:   Singlet-A      2.2578 eV  549.15 nm  f=0.0518 >     495 -> 499       -0.13275 >     496 -> 498        0.60862 >     496 -> 500        0.14546 >     497 -> 499       -0.25852 > > I understand that 2.2578 eV is the excitation energy. f=0.0518 is oscillator strength (proportional to the intensity of excitation). 495->499 are orbitals excited from and to. -0.13275 is the coefficient of the wavefunction for each excitation. > > My question is: Why this excitation coefficient is negative? When I calculate the excitation probability is the probability of excitation from 495 to 499 3.52% or -3.52%? In some papers I saw negative excitation probability. What does it mean? > > Sincerely, > > Peter Khlyabich > ----------------------------------------------------- > University of Southern California > Chemistry Department > Prof. Barry C. Thompson Group > phone: 213-740-2599 > e-mail: khlyabic#usc.edu>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel*o*gmail.com From owner-chemistry@ccl.net Wed Aug 4 08:42:00 2010 From: "venkara suresh kumar Neelamraju nvskumar123===yahoo.co.in" To: CCL Subject: CCL: scale factor for b3lyp/6-31g(d,p) Message-Id: <-42428-100804020605-17661-T5phcj/A6T2YPawOok8Fsw * server.ccl.net> X-Original-From: "venkara suresh kumar Neelamraju" Date: Wed, 4 Aug 2010 02:06:03 -0400 Sent to CCL by: "venkara suresh kumar Neelamraju" [nvskumar123#,#yahoo.co.in] Dear CCL Members, I did not find an appropriate scale factor for vibrational frequencies calculated at b3lyp/6-31g(d,p). Please iform me if any body finds it in the literature. N V Suresh Kumar From owner-chemistry@ccl.net Wed Aug 4 09:17:00 2010 From: "Uhrig, Ulrike Ulrike.Uhrig%%certara.com" To: CCL Subject: CCL: [Tripos] CCL: Chemical database 2d to 3D convertion Message-Id: <-42429-100804032636-18511-2Eoq11JL2Tz8fvtKMoZ9kg|,|server.ccl.net> X-Original-From: "Uhrig, Ulrike" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 4 Aug 2010 02:26:22 -0500 MIME-Version: 1.0 Sent to CCL by: "Uhrig, Ulrike" [Ulrike.Uhrig : certara.com] Hi Williman, If you have concord available you might have as well stereoplex as this is all bundled in the SYBYL-X package. It generates for all chiral centers all possible stereoisomers and then you will run this output through concord. Cheers, Ulrike --- Dr. Ulrike Uhrig Application Scientist Manager & Discovery Software Trainer Tripos - A Certara(tm) Company Martin-Kollar-Str. 17 D - 81829 Muenchen -----Original Message----- > From: William Wei william.wei|,|utoronto.ca [mailto:owner-chemistry++ccl.net] Sent: Tuesday, August 03, 2010 9:28 PM To: Uhrig, Ulrike Subject: [Tripos] CCL: Chemical database 2d to 3D convertion Sent to CCL by: "William Wei" [william.wei*utoronto.ca] Hi everybody, I am looking for a 2D to 3D sdf format convert software. Better if it is free. My request is if chiral center(s) in the 2D structure did not specified, I need both S and R conformation. I used Concord, but it just generate one conformation if the chiral center is not specified. If any of you have used other software can do the job, please let me know. Any information if appreciated. Thanks, Williamhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt_________________________________________________________________ NOTICE: The information contained in this electronic mail message is intended only for the personal and confidential use of the designated recipient(s) named above. This message may be an attorney-client communication, may be protected by the work product doctrine, and may be subject to a protective order. As such, this message is privileged and confidential. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this message in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by telephone and e-mail and destroy any and all copies of this message in your possession (whether hard copies or electronically stored copies). Thank you. From owner-chemistry@ccl.net Wed Aug 4 09:52:01 2010 From: "Wilfried Langenaeker wilfried.langenaeker*silicos.com" To: CCL Subject: CCL: release of molecular filtering software Sieve Message-Id: <-42430-100804033912-21894-gDBwKSJ/+K4BQaT3ehQnYg,+,server.ccl.net> X-Original-From: "Wilfried Langenaeker" Date: Wed, 4 Aug 2010 03:39:09 -0400 Sent to CCL by: "Wilfried Langenaeker" [wilfried.langenaeker-*-silicos.com] Silicos is pleased to announce the release of version 3 of its molecular filtering software Sieve. Sieve is a program for filtering out molecules with unwanted properties. It is based on the Open Babel open source C++ API (version 2.3) for rapid calculation of molecular properties. The program comes with a number of pre-programmed molecular properties that can be used for filtering. These properties include, amongst others: Physicochemical parameters, such as logP, topological polar surface area criteria, number of hydrogen bond acceptors and donors, and Lipinski's rule-of-five; Graph-based properties, including ring-based parameters and rotatable bond criteria; Selection criteria by means of smarts patterns; Similarity criteria; Three-dimensional distances between user-definable fragments; Criteria based on molecular titles and/or SDF-tags Sieve is a command line-driven program that is instructed by means of command line options and a user-definable filter file. The source code is released under the terms of the GNU General Public License as published the Free Software Foundation version 2 of the License. It can be downloaded from www.silicos.com or openbabel.org/wiki/Related_Projects Silicos is a fee-for-service company empowering open source chemo-informatics virtual screening technologies for the discovery of novel lead compounds and database characterization. Silicos fully endorses the concept of open innovation and open source software development, and provides its clients with a wide variety of computational chemistry-based lead discovery services, including Open Babel support, training and code development. Please visit www.silicos.com for more details. From owner-chemistry@ccl.net Wed Aug 4 10:26:00 2010 From: "Charles Johnson cjohns98[A]slu.edu" To: CCL Subject: CCL: scale factor for b3lyp/6-31g(d,p) Message-Id: <-42431-100804093929-11963-ixkCTrP3PoL0qHNzRisrCw],[server.ccl.net> X-Original-From: Charles Johnson Content-Type: multipart/alternative; boundary=00163630ff2fad496f048cff8f43 Date: Wed, 4 Aug 2010 08:39:21 -0500 MIME-Version: 1.0 Sent to CCL by: Charles Johnson [cjohns98(~)slu.edu] --00163630ff2fad496f048cff8f43 Content-Type: text/plain; charset=ISO-8859-1 The book entitled Essentials of Computational Chemistry by Cramer, Wiley, 2004, has a fairly comprehensive table of scaling factors. Hope this helps. Charles Johnson On Wed, Aug 4, 2010 at 1:06 AM, venkara suresh kumar Neelamraju nvskumar123===yahoo.co.in wrote: > > Sent to CCL by: "venkara suresh kumar Neelamraju" [nvskumar123#,# > yahoo.co.in] > Dear CCL Members, > > I did not find an appropriate scale factor for vibrational frequencies > calculated at b3lyp/6-31g(d,p). Please iform me if any body finds it in the > literature. > > N V Suresh Kumar> > > -- Charles A. Johnson Graduate Student Department of Chemistry Saint Louis University --00163630ff2fad496f048cff8f43 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable The book entitled Essentials of Computational Chemistry by Cramer, Wiley, 2= 004, has a fairly comprehensive table of scaling factors.

Hope this = helps.

Charles Johnson

On Wed, Aug= 4, 2010 at 1:06 AM, venkara suresh kumar Neelamraju nvskumar123=3D=3D=3Dyahoo.co.in <owner-chemistry**ccl.net> = wrote:

Sent to CCL by: "venkara suresh kumar Neelamraju" [nvskumar123#,#= yahoo.co.in]
Dear CCL Members,

I did not find an appropriate scale factor for vibrational frequencies calc= ulated at b3lyp/6-31g(d,p). Please iform me if any body finds it in the lit= erature.

N V Suresh Kumar



-=3D This is automatically added to each message by the mailing script =3D-=
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--
Charles A. Johnson
G= raduate Student
Department of Chemistry
Saint Louis University

--00163630ff2fad496f048cff8f43-- From owner-chemistry@ccl.net Wed Aug 4 11:45:01 2010 From: "Oellien, F (Frank) frank.oellien^-^sp.intervet.com" To: CCL Subject: CCL: 2nd Call for Papers - GCC2010 Message-Id: <-42432-100804104319-16643-p7TKD6LgLjpi3S91RiBNdA|a|server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 4 Aug 2010 16:43:10 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [frank.oellien]=[sp.intervet.com] 2nd CALL FOR PAPERS 6th German Conference on Chemoinformatics Hotel 'Der Achtermann', Goslar, Germany 7 - 9 November 2010 Dear Colleagues, The CIC division of the German Chemical Society announces the 6. German Conference on Chemoinformatics (http://www.gdch.de/gcc2010) to be held in Goslar, Germany, November 7 - 9, 2010. We have extended the deadline for abstract submission until August 13, 2010!! We are inviting the submission of abstracts for talks and posters in the following plenary sessions: * Chemoinformatics and Drug Discovcery * Chemical Information, Patents, and Databases * Molecular Modelling * Computational Material Science and Nanotechnology In addition other highlights in the field of Computational Chemistry are also welcome. Invited Speakers this year are: * Colleen Fitzpatrick, Identifiers International, Huntington Beach, USA * Gerhard Klebe, University of Marburg, DE * Holger Gohlke, University of Düsseldorf, DE * Jürgen Gmehling, University of Oldenburg, DE * Hans Fraaije, University of Leiden, NL * Wolfang Guba, Roche, Basel, CH * Andrew R. Leach, GSK, Stevenage, UK Visit the conference website at www.gdch.de/gcc2010 for more information or access directly the Call-for-Paper PDF http://www.gdch.de/vas/tagungen/tg/einlad5412.pdf The extended deadline for the submission of abstracts is 13 August 2010! I hope to see you in Goslar again. Frank Oellien GDCh CIC Chair Mit freundlichen Grüßen / With kind regards Dr. Frank Oellien BioChemInformatics Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien(0)sp.intervet.com Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.intervet.com A subsidiary of Merck & Co., Inc., Whitehouse Station, NJ, USA Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid From owner-chemistry@ccl.net Wed Aug 4 12:20:00 2010 From: "Cheri McFerrin cmcfer1-#-tigers.lsu.edu" To: CCL Subject: CCL: scale factor for b3lyp/6-31g(d,p) Message-Id: <-42433-100804104752-21807-qcQqvXOXLkucMGqhMnWLkw]^[server.ccl.net> X-Original-From: Cheri McFerrin Content-Type: multipart/alternative; boundary=0016364d2c1f43738e048d008445 Date: Wed, 4 Aug 2010 09:47:45 -0500 MIME-Version: 1.0 Sent to CCL by: Cheri McFerrin [cmcfer1+*+tigers.lsu.edu] --0016364d2c1f43738e048d008445 Content-Type: text/plain; charset=ISO-8859-1 go to cccbdb.nist.gov. then click on III. Calculated Data. Next, go to section B. cheri On Wed, Aug 4, 2010 at 1:06 AM, venkara suresh kumar Neelamraju nvskumar123===yahoo.co.in wrote: > > Sent to CCL by: "venkara suresh kumar Neelamraju" [nvskumar123#,# > yahoo.co.in] > Dear CCL Members, > > I did not find an appropriate scale factor for vibrational frequencies > calculated at b3lyp/6-31g(d,p). Please iform me if any body finds it in the > literature. > > N V Suresh Kumar> > > --0016364d2c1f43738e048d008445 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable go to cccbdb.nist.gov. =A0then click= on III. Calculated Data. =A0 Next, go to section B.

che= ri


On Wed, Aug= 4, 2010 at 1:06 AM, venkara suresh kumar Neelamraju nvskumar123=3D=3D=3Dyahoo.co.in <owner-chemistry .. ccl.net> = wrote:

Sent to CCL by: "venkara suresh kumar Neelamraju" [nvskumar123#,#= yahoo.co.in]
Dear CCL Members,

I did not find an appropriate scale factor for vibrational frequencies calc= ulated at b3lyp/6-31g(d,p). Please iform me if any body finds it in the lit= erature.

N V Suresh Kumar

--0016364d2c1f43738e048d008445-- From owner-chemistry@ccl.net Wed Aug 4 12:55:01 2010 From: "Tatsiana Kirys nushki#,#mail.ru" To: CCL Subject: CCL: =?koi8-r?Q?Re=3A_CCL=3A_charmm_energy?= Message-Id: <-42434-100804115818-10305-UGDCcJVilowrepIFmAWPkQ]^[server.ccl.net> X-Original-From: Tatsiana Kirys Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=koi8-r Date: Wed, 04 Aug 2010 19:58:10 +0400 Mime-Version: 1.0 Sent to CCL by: Tatsiana Kirys [nushki||mail.ru] thank you!!! i'll try that Tue, 3 Aug 2010 22:36:24 -0700 (PDT) ÐÉÓØÍÏ ÏÔ "Visvaldas K. coyote_v2002 * yahoo.com" : > > I am not sure if this is of much help, but I couldn't help noticing that the calculations are done using perl script, so by analyzing what commands or components are activated when using different flags you could try to figure out the reasons for the discrepancy yourself. Sorry I can't help more here much since we don't have CHARMM. > Vis Kairys > > > > > > > Sent to CCL by: "Tatsiana Kirys" [tatsiana%x%ku.edu] > > Hi all, > > > > i calculate protein energy using enrCHARMM.pl script. i run it with gb and without for the same protein file. > > > > enerCHARMM.pl -out total -log file.log file.pdb > > BONDs 92.56954 > > ANGLes 336.00337 > > UREY-b 24.08096 > > DIHEdrals 604.46805 > > CMAPs -134.62511 > > VDWaals -476.01682 > > ELEC -2041.80015 > > > > > > enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb > > > > BONDs 92.56954 > > ANGLes 336.00337 > > UREY-b 24.08096 > > DIHEdrals 604.46805 > > CMAPs -134.62511 > > VDWaals -485.01639 > > ELEC -2021.31359 > > ASP 102.42587 > > GBEnr -1479.15727 > > > > i dont understand why Electrostatic and VdW energy terms are different. Any help will be very appreciated!!!ñ × íÏÅÍ íÉÒÅ - http://my.mail.ru/mail/nushki/> > E-mail to subscribers: CHEMISTRY(!)ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net or use> > > > > > > -- > Mahmoud A. A. Ibrahim > Current Address > 7.05, School of Chemistry, > The University of Manchester, > Oxford Road, Manchester, M13 9PL, > United Kingdom. > > Home Address > Chemistry Department, > Faculty of Science, > Minia University, > Minia 61519, > Egypt. > > Contact Information > Email: m.ibrahim(!)compchem.net > Website: www.compchem.net > Fax No.: +20862342601 ñ × íÏÅÍ íÉÒÅ - http://my.mail.ru/mail/nushki/ From owner-chemistry@ccl.net Wed Aug 4 13:30:01 2010 From: "Tatsiana Kirys nushki!A!mail.ru" To: CCL Subject: CCL: =?koi8-r?Q?Re=3A_CCL=3A_charmm_energy?= Message-Id: <-42435-100804120905-17543-NDaxASCS/q4W9rW4NM6U1Q%server.ccl.net> X-Original-From: Tatsiana Kirys Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=koi8-r Date: Wed, 04 Aug 2010 20:08:31 +0400 Mime-Version: 1.0 Sent to CCL by: Tatsiana Kirys [nushki(0)mail.ru] Dear Mr Ibrahim in case of "gb" the software uses Generalized Born equation and that is why we have additional term "GBEnr" which is as far as i understand electrostatic solvation energy and hence Elec must be vacuum electrostatics. I'm wondering why would they use different atomic radii(if they did)? in perl script i didnt find any clues for different radius. Tue, 3 Aug 2010 21:59:37 +0100 ÐÉÓØÍÏ ÏÔ "Mahmoud A. A. Ibrahim m.ibrahim(~)compchem.net" : > Dear Tatsiana > I don't know what the default method is used when you don't specify gb "-par gb". > > All what I can do is to inform you that this may be returned to the atomic radii used during the calculation, "different radii give different binding energies > > In addition to the equation used for solvation free enegy calculation and electrostatic contribution. Sure, Eele will be different, for example, in case of "gb" the software uses Generalized Born equation, and in case of the default option the software uses another equation like Poisson Boltzmann equation, this leads to a variation in the binding energy too. > > > For just a thread to follow: "Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf" > > > Hope it may be helpful > > Sincerely; > > M. Ibrahim > > > > in addition to the equation used for solvation free energy calculation "Generalized Born in case of GB, or another > Tatsiana > > 2010/8/3 Tatsiana Kirys nushki~~mail.ru > > Sent to CCL by: Tatsiana Kirys [nushki!=!mail.ru] > > I posted it to MMTSB forum at charmm.org (http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=24980#Post24980) > > but nobody answers it. > > I'd appreciate your help! > > Tatsiana Kirys > PhD student in bioinformatics > > Thu, 29 Jul 2010 18:23:24 -0400 ÐÉÓØÍÏ ÏÔ "Venable, Richard (NIH/NHLBI) E venabler^^^nhlbi.nih.gov" : > > > > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler:+:nhlbi.nih.gov] > > I suggest posting your question to the MMTSB forum at www.charmm.org > > > > -- > > Rick Venable 5635 FL/T906 > > Membrane Biophysics Section > > NIH/NHLBI Lab. of Computational Biology > > Bethesda, MD 20892-9314 U.S.A. > > > > > > On 7/29/10 4:40 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: > > > > > > > > Sent to CCL by: "Tatsiana Kirys" [tatsiana%x%ku.edu] > > Hi all, > > > > i calculate protein energy using enrCHARMM.pl script. i run it with gb and without for the same protein file. > > > > enerCHARMM.pl -out total -log file.log file.pdb > > BONDs 92.56954 > > ANGLes 336.00337 > > UREY-b 24.08096 > > DIHEdrals 604.46805 > > CMAPs -134.62511 > > VDWaals -476.01682 > > ELEC -2041.80015 > > > > > > enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb > > > > BONDs 92.56954 > > ANGLes 336.00337 > > UREY-b 24.08096 > > DIHEdrals 604.46805 > > CMAPs -134.62511 > > VDWaals -485.01639 > > ELEC -2021.31359 > > ASP 102.42587 > > GBEnr -1479.15727 > > > > i dont understand why Electrostatic and VdW energy terms are different. Any help will be very appreciated!!!ñ × íÏÅÍ íÉÒÅ - http://my.mail.ru/mail/nushki/> E-mail to subscribers: CHEMISTRY(!)ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net or use> > > > > > > -- > Mahmoud A. A. Ibrahim > Current Address > 7.05, School of Chemistry, > The University of Manchester, > Oxford Road, Manchester, M13 9PL, > United Kingdom. > > Home Address > Chemistry Department, > Faculty of Science, > Minia University, > Minia 61519, > Egypt. > > Contact Information > Email: m.ibrahim(!)compchem.net > Website: www.compchem.net > Fax No.: +20862342601 ñ × íÏÅÍ íÉÒÅ - http://my.mail.ru/mail/nushki/ From owner-chemistry@ccl.net Wed Aug 4 16:55:01 2010 From: "Venable, Richard (NIH/NHLBI) E venabler|nhlbi.nih.gov" To: CCL Subject: CCL: charmm energy Message-Id: <-42436-100804142457-27946-VnuubneqKp0u71cLiWQJbA~~server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="windows-1251" Date: Wed, 4 Aug 2010 14:19:59 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler[*]nhlbi.nih.gov] Please read the CHARMM documentation files gbsw.doc and gbmv.doc (and references therein) for some ideas about how GB methods work, and why they might have some dependence on radii choices. The GB methods also require different truncation methods and cutoffs than the standard parameter set default methods and cutoffs, which are intended for use with explicit TIP3 water instead of an implicit water model. Also, please note that it might take a few days for someone associated with the MMTSB suite of perl scripts to answer your posts at www.charmm.org, now that they are finally in the correct forum. And besides, people do tend to take vacations in August ... Regards, -- Rick Venable 5635 FL/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 8/4/10 12:08 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: Sent to CCL by: Tatsiana Kirys [nushki(0)mail.ru] Dear Mr Ibrahim in case of "gb" the software uses Generalized Born equation and that is why we have additional term "GBEnr" which is as far as i understand electrostatic solvation energy and hence Elec must be vacuum electrostatics. I'm wondering why would they use different atomic radii(if they did)? in perl script i didnt find any clues for different radius. Tue, 3 Aug 2010 21:59:37 +0100 ïèñüìî îò "Mahmoud A. A. Ibrahim m.ibrahim(~)compchem.net" : > Dear Tatsiana > I don't know what the default method is used when you don't specify gb "-par gb". > > All what I can do is to inform you that this may be returned to the atomic radii used during the calculation, "different radii give different binding energies > > In addition to the equation used for solvation free enegy calculation and electrostatic contribution. Sure, Eele will be different, for example, in case of "gb" the software uses Generalized Born equation, and in case of the default option the software uses another equation like Poisson Boltzmann equation, this leads to a variation in the binding energy too. > > > For just a thread to follow: "Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf" > > > Hope it may be helpful > > Sincerely; > > M. Ibrahim > > > > in addition to the equation used for solvation free energy calculation "Generalized Born in case of GB, or another > Tatsiana > > 2010/8/3 Tatsiana Kirys nushki~~mail.ru > > Sent to CCL by: Tatsiana Kirys [nushki!=!mail.ru] > > I posted it to MMTSB forum at charmm.org (http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=24980#Post24980) > > but nobody answers it. > > I'd appreciate your help! > > Tatsiana Kirys > PhD student in bioinformatics > > Thu, 29 Jul 2010 18:23:24 -0400 ïèñüìî îò "Venable, Richard (NIH/NHLBI) E venabler^^^nhlbi.nih.gov" : > > > > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler:+:nhlbi.nih.gov] > > I suggest posting your question to the MMTSB forum at www.charmm.org > > > > -- > > Rick Venable 5635 FL/T906 > > Membrane Biophysics Section > > NIH/NHLBI Lab. of Computational Biology > > Bethesda, MD 20892-9314 U.S.A. > > > > > > On 7/29/10 4:40 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: > > > > > > > > Sent to CCL by: "Tatsiana Kirys" [tatsiana%x%ku.edu] > > Hi all, > > > > i calculate protein energy using enrCHARMM.pl script. i run it with gb and without for the same protein file. > > > > enerCHARMM.pl -out total -log file.log file.pdb > > BONDs 92.56954 > > ANGLes 336.00337 > > UREY-b 24.08096 > > DIHEdrals 604.46805 > > CMAPs -134.62511 > > VDWaals -476.01682 > > ELEC -2041.80015 > > > > > > enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb > > > > BONDs 92.56954 > > ANGLes 336.00337 > > UREY-b 24.08096 > > DIHEdrals 604.46805 > > CMAPs -134.62511 > > VDWaals -485.01639 > > ELEC -2021.31359 > > ASP 102.42587 > > GBEnr -1479.15727 > > > > i dont understand why Electrostatic and VdW energy terms are different. Any help will be very appreciated!!!ß â Ìîåì Ìèðå - http://my.mail.ru/mail/nushki/> E-mail to subscribers: CHEMISTRY(!)ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net or use> > > > > > > -- > Mahmoud A. A. Ibrahim > Current Address > 7.05, School of Chemistry, > The University of Manchester, > Oxford Road, Manchester, M13 9PL, > United Kingdom. > > Home Address > Chemistry Department, > Faculty of Science, > Minia University, > Minia 61519, > Egypt. > > Contact Information > Email: m.ibrahim(!)compchem.net > Website: www.compchem.net > Fax No.: +20862342601 ß â Ìîåì Ìèðå - http://my.mail.ru/mail/nushki/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Aug 4 17:30:01 2010 From: "Vijay Tak takvijay(~)gmail.com" To: CCL Subject: CCL: Conformation of trication Message-Id: <-42437-100804134147-17787-vfgBFYMtKZa1tbBrWP/VKw+/-server.ccl.net> X-Original-From: "Vijay Tak" Date: Wed, 4 Aug 2010 13:41:46 -0400 Sent to CCL by: "Vijay Tak" [takvijay%x%gmail.com] Hi CCL, I am very new to computational chemistry. Please help me out.I would like to find the minimum energy conformation of imidazolium based trication ( total 86 atoms).Let me know which software is suitable in this case. Is Discovery studio is appropriate for for this task. Thanks, Vijay Tak takvijay=-=gmail.com From owner-chemistry@ccl.net Wed Aug 4 20:18:00 2010 From: "Tatsiana Kirys nushki..mail.ru" To: CCL Subject: CCL: =?koi8-r?Q?Re=3A_CCL=3A_charmm_energy?= Message-Id: <-42438-100804182446-16731-n6CUgJbOmCBfxrr94YZDNA:server.ccl.net> X-Original-From: Tatsiana Kirys Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=koi8-r Date: Thu, 05 Aug 2010 02:24:37 +0400 Mime-Version: 1.0 Sent to CCL by: Tatsiana Kirys [nushki~~mail.ru] thank you, ill read them! Wed, 4 Aug 2010 14:19:59 -0400 ÐÉÓØÍÏ ÏÔ "Venable, Richard (NIH/NHLBI) E venabler|nhlbi.nih.gov" : > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler[*]nhlbi.nih.gov] > Please read the CHARMM documentation files gbsw.doc and gbmv.doc (and references therein) for some ideas about how GB methods work, and why they might have some dependence on radii choices. The GB methods also require different truncation methods and cutoffs than the standard parameter set default methods and cutoffs, which are intended for use with explicit TIP3 water instead of an implicit water model. > > Also, please note that it might take a few days for someone associated with the MMTSB suite of perl scripts to answer your posts at www.charmm.org, now that they are finally in the correct forum. And besides, people do tend to take vacations in August ... > > Regards, > > -- > Rick Venable 5635 FL/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 8/4/10 12:08 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: > > > > Sent to CCL by: Tatsiana Kirys [nushki(0)mail.ru] > Dear Mr Ibrahim > > in case of "gb" the software uses Generalized Born equation and that is why we have additional term "GBEnr" which is as far as i understand electrostatic solvation energy and hence Elec must be vacuum electrostatics. > > I'm wondering why would they use different atomic radii(if they did)? in perl script i didnt find any clues for different radius. > > > > Tue, 3 Aug 2010 21:59:37 +0100 ÐÉÓØÍÏ ÏÔ "Mahmoud A. A. Ibrahim m.ibrahim(~)compchem.net" : > > > Dear Tatsiana > > I don't know what the default method is used when you don't specify gb "-par gb". > > > > All what I can do is to inform you that this may be returned to the atomic radii used during the calculation, "different radii give different binding energies > > > > In addition to the equation used for solvation free enegy calculation and electrostatic contribution. Sure, Eele will be different, for example, in case of "gb" the software uses Generalized Born equation, and in case of the default option the software uses another equation like Poisson Boltzmann equation, this leads to a variation in the binding energy too. > > > > > > For just a thread to follow: "Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf" > > > > > > Hope it may be helpful > > > > Sincerely; > > > > M. Ibrahim > > > > > > > > in addition to the equation used for solvation free energy calculation "Generalized Born in case of GB, or another > > Tatsiana > > > > 2010/8/3 Tatsiana Kirys nushki~~mail.ru > > > > Sent to CCL by: Tatsiana Kirys [nushki!=!mail.ru] > > > > I posted it to MMTSB forum at charmm.org (http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=24980#Post24980) > > > > but nobody answers it. > > > > I'd appreciate your help! > > > > Tatsiana Kirys > > PhD student in bioinformatics > > > > Thu, 29 Jul 2010 18:23:24 -0400 ÐÉÓØÍÏ ÏÔ "Venable, Richard (NIH/NHLBI) E venabler^^^nhlbi.nih.gov" : > > > > > > > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler:+:nhlbi.nih.gov] > > > I suggest posting your question to the MMTSB forum at www.charmm.org > > > > > > -- > > > Rick Venable 5635 FL/T906 > > > Membrane Biophysics Section > > > NIH/NHLBI Lab. of Computational Biology > > > Bethesda, MD 20892-9314 U.S.A. > > > > > > > > > On 7/29/10 4:40 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: > > > > > > > > > > > > Sent to CCL by: "Tatsiana Kirys" [tatsiana%x%ku.edu] > > > Hi all, > > > > > > i calculate protein energy using enrCHARMM.pl script. i run it with gb and without for the same protein file. > > > > > > enerCHARMM.pl -out total -log file.log file.pdb > > > BONDs 92.56954 > > > ANGLes 336.00337 > > > UREY-b 24.08096 > > > DIHEdrals 604.46805 > > > CMAPs -134.62511 > > > VDWaals -476.01682 > > > ELEC -2041.80015 > > > > > > > > > enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb > > > > > > BONDs 92.56954 > > > ANGLes 336.00337 > > > UREY-b 24.08096 > > > DIHEdrals 604.46805 > > > CMAPs -134.62511 > > > VDWaals -485.01639 > > > ELEC -2021.31359 > > > ASP 102.42587 > > > GBEnr -1479.15727 > > > > > > i dont understand why Electrostatic and VdW energy terms are different. Any help will be very appreciated!!!ñ × íÏÅÍ íÉÒÅ - http://my.mail.ru/mail/nushki/> E-mail to subscribers: CHEMISTRY(!)ccl.net or use:> > > E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net or use> > > > > > > > > > > > > -- > > Mahmoud A. A. Ibrahim > > Current Address > > 7.05, School of Chemistry, > > The University of Manchester, > > Oxford Road, Manchester, M13 9PL, > > United Kingdom. > > > > Home Address > > Chemistry Department, > > Faculty of Science, > > Minia University, > > Minia 61519, > > Egypt. > > > > Contact Information > > Email: m.ibrahim(!)compchem.net > > Website: www.compchem.net > > Fax No.: +20862342601 > > > ñ × íÏÅÍ íÉÒÅ - http://my.mail.ru/mail/nushki/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtJade Dynasty - ÒÅ×ÏÌÀÃÉÑ × ÍÉÒÅ ÒÏÌÅ×ÙÈ ÉÇÒ! éÇÒÁÊ ÎÁ Mail.ru! http://r.mail.ru/cln7681/jd.mail.ru/promo From owner-chemistry@ccl.net Wed Aug 4 20:53:00 2010 From: "rumi s du durumi08,,gmail.com" To: CCL Subject: CCL: How to handle metal ion in docking run? Message-Id: <-42439-100804195306-27754-/XpCIFhiSbd64I78zd8lHw||server.ccl.net> X-Original-From: "rumi s du" Date: Wed, 4 Aug 2010 19:53:04 -0400 Sent to CCL by: "rumi s du" [durumi08{=}gmail.com] I'm planning to do virtual screening. I can use Accelrys sofrware and GOLD. I found how to handle metal in GOLD, so i tried, but the geometry is not as I want. (It's octahedral as i want, but position of 6 pseudo-H-bond-donor points are not as i expected.) According to the reference, 3 aroms of protein are interacting with this metal, but the structure fail to find 2 coordinating partners. Maybe because the b-factor around metal is too high, like around 70. So is there anyway I can assign coordinating protein atoms in GOLD? or any other way (program or other recommend) to handle metal in docking study? From owner-chemistry@ccl.net Wed Aug 4 21:28:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim++compchem.net" To: CCL Subject: CCL: charmm energy Message-Id: <-42440-100804204933-27010-ShQ4AqgMEs482NVYDkxPDA * server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=001636459042c84c8f048d08ebaf Date: Thu, 5 Aug 2010 01:49:21 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim]^[compchem.net] --001636459042c84c8f048d08ebaf Content-Type: text/plain; charset=KOI8-R Content-Transfer-Encoding: quoted-printable Dear Tatsiana I am so sorry, may be my reply wasn't helpful enough, due to I haven't worked with Charmm before and I am not familiar with the default parameters used. About radii, yes, the GBSA results change with changing the atomic radii, a= s I know in AMBER, mbondi2 radii is recommended for GBSA calculation. This point is covered in the paper (Converging Free Energy Estimates: MM-PB(GB)S= A Studies on the Protein-Protein Complex Ras-Raf) Sincerely; M. Ibrahm 2010/8/4 Tatsiana Kirys nushki..mail.ru > > Sent to CCL by: Tatsiana Kirys [nushki~~mail.ru] > > > thank you, ill read them! > > Wed, 4 Aug 2010 14:19:59 -0400 =D0=C9=D3=D8=CD=CF =CF=D4 "Venable, Richar= d (NIH/NHLBI) E > venabler|nhlbi.nih.gov" : > > > > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler[*] > nhlbi.nih.gov] > > Please read the CHARMM documentation files gbsw.doc and gbmv.doc (and > references therein) for some ideas about how GB methods work, and why the= y > might have some dependence on radii choices. The GB methods also require > different truncation methods and cutoffs than the standard parameter set > default methods and cutoffs, which are intended for use with explicit TIP= 3 > water instead of an implicit water model. > > > > Also, please note that it might take a few days for someone associated > with the MMTSB suite of perl scripts to answer your posts at > www.charmm.org, now that they are finally in the correct forum. And > besides, people do tend to take vacations in August ... > > > > Regards, > > > > -- > > Rick Venable 5635 FL/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 8/4/10 12:08 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" > wrote: > > > > > > > > Sent to CCL by: Tatsiana Kirys [nushki(0)mail.ru] > > Dear Mr Ibrahim > > > > in case of "gb" the software uses Generalized Born equation and that is > why we have additional term "GBEnr" which is as far as i understand > electrostatic solvation energy and hence Elec must be vacuum electrostati= cs. > > > > I'm wondering why would they use different atomic radii(if they did)? i= n > perl script i didnt find any clues for different radius. > > > > > > > > Tue, 3 Aug 2010 21:59:37 +0100 =D0=C9=D3=D8=CD=CF =CF=D4 "Mahmoud A. A.= Ibrahim > m.ibrahim(~)compchem.net" : > > > > > Dear Tatsiana > > > I don't know what the default method is used when you don't specify g= b > "-par gb". > > > > > > All what I can do is to inform you that this may be returned to the > atomic radii used during the calculation, "different radii give different > binding energies > > > > > > In addition to the equation used for solvation free enegy calculation > and electrostatic contribution. Sure, Eele will be different, for example= , > in case of "gb" the software uses Generalized Born equation, and in case = of > the default option the software uses another equation like Poisson Boltzm= ann > equation, this leads to a variation in the binding energy too. > > > > > > > > > For just a thread to follow: "Converging Free Energy Estimates: > MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf" > > > > > > > > > Hope it may be helpful > > > > > > Sincerely; > > > > > > M. Ibrahim > > > > > > > > > > > > in addition to the equation used for solvation free energy calculatio= n > "Generalized Born in case of GB, or another > > > Tatsiana > > > > > > 2010/8/3 Tatsiana Kirys nushki~~mail.ru > > > > > > Sent to CCL by: Tatsiana Kirys [nushki!=3D!mail.ru] > > > > > > I posted it to MMTSB forum at charmm.org ( > http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=3Dshowflat&Numb= er=3D24980#Post24980 > ) > > > > > > but nobody answers it. > > > > > > I'd appreciate your help! > > > > > > Tatsiana Kirys > > > PhD student in bioinformatics > > > > > > Thu, 29 Jul 2010 18:23:24 -0400 =D0=C9=D3=D8=CD=CF =CF=D4 "Venable, R= ichard (NIH/NHLBI) > E venabler^^^nhlbi.nih.gov" : > > > > > > > > > > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler:+: > nhlbi.nih.gov] > > > > I suggest posting your question to the MMTSB forum at www.charmm.or= g > > > > > > > > -- > > > > Rick Venable 5635 FL/T906 > > > > Membrane Biophysics Section > > > > NIH/NHLBI Lab. of Computational Biology > > > > Bethesda, MD 20892-9314 U.S.A. > > > > > > > > > > > > On 7/29/10 4:40 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" > wrote: > > > > > > > > > > > > > > > > Sent to CCL by: "Tatsiana Kirys" [tatsiana%x%ku.edu] > > > > Hi all, > > > > > > > > i calculate protein energy using enrCHARMM.pl script. i run it with > gb and without for the same protein file. > > > > > > > > enerCHARMM.pl -out total -log file.log file.pdb > > > > BONDs 92.56954 > > > > ANGLes 336.00337 > > > > UREY-b 24.08096 > > > > DIHEdrals 604.46805 > > > > CMAPs -134.62511 > > > > VDWaals -476.01682 > > > > ELEC -2041.80015 > > > > > > > > > > > > enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb > > > > > > > > BONDs 92.56954 > > > > ANGLes 336.00337 > > > > UREY-b 24.08096 > > > > DIHEdrals 604.46805 > > > > CMAPs -134.62511 > > > > VDWaals -485.01639 > > > > ELEC -2021.31359 > > > > ASP 102.42587 > > > > GBEnr -1479.15727 > > > > > > > > i dont understand why Electrostatic and VdW energy terms are > different. Any help will be very appreciated!!!=F1 =D7 =ED=CF=C5=CD =ED= =C9=D2=C5 - > http://my.mail.ru/mail/nushki/> E-mail to subscribers: CHEMISTRY(!)ccl.ne= tor use:> > > > E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net or use> > > > > > > > > > > > > > > > > > > -- > > > Mahmoud A. A. Ibrahim > > > Current Address > > > 7.05, School of Chemistry, > > > The University of Manchester, > > > Oxford Road, Manchester, M13 9PL, > > > United Kingdom. > > > > > > Home Address > > > Chemistry Department, > > > Faculty of Science, > > > Minia University, > > > Minia 61519, > > > Egypt. > > > > > > Contact Information > > > Email: m.ibrahim(!)compchem.net > > > Website: www.compchem.net > > > Fax No.: +20862342601 > > > > > > =F1 =D7 =ED=CF=C5=CD =ED=C9=D2=C5 - > http://my.mail.ru/mail/nushki/http://www.ccl.net/cgi-bin/ccl/send_ccl_mes= sagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers= .txtJadeDynasty - =D2=C5=D7=CF=CC=C0=C3=C9=D1 =D7 =CD=C9=D2=C5 =D2=CF=CC=C5= =D7=D9=C8 =C9=C7=D2! =E9=C7=D2=C1=CA =CE=C1 Mail.ru! > http://r.mail.ru/cln7681/jd.mail.ru/promo > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim+*+compchem.net Website: www.compchem.net Fax No.: +20862342601 --001636459042c84c8f048d08ebaf Content-Type: text/html; charset=KOI8-R Content-Transfer-Encoding: quoted-printable Dear Tatsiana
I am so sorry, may be my reply wasn't helpful enough,= due to I haven't worked with Charmm before and I am not familiar with = the=9Adefault=9Aparameters=9Aused.
About radii, yes, the GBSA res= ults change with changing the atomic radii, as I know in AMBER, mbondi2 rad= ii is recommended for GBSA calculation. This point is covered in the paper = (Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Prote= in Complex Ras-Raf)
Sincerely;
M. Ibrahm

2010/8/4 Tatsiana Kirys nushki..mail.ru <owner-chemis= try+*+ccl.net>

Sent to CCL by: Tatsiana Kirys [nushki~~mail.ru]


thank you, ill read them!

Wed, 4 Aug 2010 14:19:59 -0400 =D0=C9=D3=D8=CD=CF =CF=D4 "Venable, Ric= hard (NIH/NHLBI) E venabler|nhlbi.nih.gov" <owner-chemistry~~ccl.net>:

>
> Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler= [*]nhlbi.nih.gov]
> Please read the CHARMM documentation files gbsw.doc and gbmv.doc= (and references therein) for some ideas about how GB methods work, and why= they might have some dependence on radii choices. =9AThe GB methods also r= equire different truncation methods and cutoffs than the standard parameter= set default methods and cutoffs, which are intended for use with explicit = TIP3 water instead of an implicit water model.
>
> Also, please note that it might take a few days for someone associated= with the MMTSB suite of perl scripts to answer your posts at www.charmm.org, now that they ar= e finally in the correct forum. =9AAnd besides, people do tend to take vaca= tions in August ...
>
> Regards,
>
> --
> Rick Venable =9A =9A 5635 FL/T906
> Membrane Biophysics Section
> NIH/NHLBI Lab. of Computational Biology
> Bethesda, MD =9A20892-9314 =9A U.S.A.
> (301) 496-1905 =9A venabler AT nhlbi*nih*gov
>
>
> On 8/4/10 12:08 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" <owner-chemistry,+,ccl.net> wrote:
>
>
>
> Sent to CCL by: Tatsiana Kirys [nushki(0)mail.ru]
> Dear Mr Ibrahim
>
> in case of "gb" the software uses Generalized Born equation = and that is why we have additional term "GBEnr" which is as far a= s i understand electrostatic solvation energy and hence Elec must be vacuum= electrostatics.
>
> I'm wondering why would they use different atomic radii(if they di= d)? in perl script i didnt find any clues for different radius.
>
>
>
> Tue, 3 Aug 2010 21:59:37 +0100 =D0=C9=D3=D8=CD=CF =CF=D4 "Mahmoud= A. A. Ibrahim m.ibrahim(~)compchem.net" <owner-chemistry|-|ccl.net>:
>
> > Dear Tatsiana
> > I don't know what the default method is used when you don'= ;t specify gb "-par gb".
> >
> > All what I can do is to inform you that this may be returned to t= he atomic radii used during the calculation, "different radii give dif= ferent binding energies
> >
> > In addition to the equation used for solvation free enegy calcula= tion and electrostatic contribution. Sure, Eele will be different, for exam= ple, in case of "gb" the software uses Generalized Born equation,= and in case of the default option the software uses another equation like = Poisson Boltzmann equation, this leads to a variation in the binding energy= too.
> >
> >
> > For just a thread to follow: "Converging Free Energy Estimat= es: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf"
> >
> >
> > Hope it may be helpful
> >
> > Sincerely;
> >
> > M. Ibrahim
> >
> >
> >
> > in addition to the equation used for solvation free energy calcul= ation "Generalized Born in case of GB, or another
> > Tatsiana
> >
> > 2010/8/3 Tatsiana Kirys nushki~~mail.ru <owner-chemistry(!)ccl.net>
> >
> > Sent to CCL by: Tatsiana Kirys [nushki!=3D!mail.ru]
> >
> > I posted it to MMTSB forum at charmm.org (http://www.charmm.org/ubbthreads-7-5-5/ubbth= reads.php?ubb=3Dshowflat&Number=3D24980#Post24980)
> >
> > but nobody answers it.
> >
> > I'd appreciate your help!
> >
> > Tatsiana Kirys
> > PhD student in bioinformatics
> >
> > Thu, 29 Jul 2010 18:23:24 -0400 =D0=C9=D3=D8=CD=CF =CF=D4 "V= enable, Richard (NIH/NHLBI) E venabler^^^nhlbi.nih.gov" <owner-chemistry[a]ccl.net>:
> >
> > >
> > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]"= [venabler:+:nhlbi.nih.g= ov]
> > > I suggest posting your question to the MMTSB forum at www.charmm.org
> > >
> > > --
> > > Rick Venable =9A =9A 5635 FL/T906
> > > Membrane Biophysics Section
> > > NIH/NHLBI Lab. of Computational Biology
> > > Bethesda, MD =9A20892-9314 =9A U.S.A.
> > >
> > >
> > > On 7/29/10 4:40 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" <owner-che= mistry(a)ccl.net> wrote= :
> > >
> > >
> > >
> > > Sent to CCL by: &quo= t;Tatsiana =9AKirys" [tatsiana%x%ku.edu]
> > > Hi all,
> > >
> > > i calculate protein energy using enrCHARMM.pl script. i run = it with gb and without for the same protein file.
> > >
> > > enerCHARMM.pl -out total -log file.log file.pdb
> > > BONDs =9A =9A =9A =9A92.56954
> > > ANGLes =9A =9A =9A336.00337
> > > UREY-b =9A =9A =9A 24.08096
> > > DIHEdrals =9A 604.46805
> > > CMAPs =9A =9A =9A-134.62511
> > > VDWaals =9A =9A-476.01682
> > > ELEC =9A =9A =9A-2041.80015
> > >
> > >
> > > enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb > > >
> > > BONDs =9A =9A =9A =9A92.56954
> > > ANGLes =9A =9A =9A336.00337
> > > UREY-b =9A =9A =9A 24.08096
> > > DIHEdrals =9A 604.46805
> > > CMAPs =9A =9A =9A-134.62511
> > > VDWaals =9A =9A-485.01639
> > > ELEC =9A =9A =9A-2021.31359
> > > ASP =9A =9A =9A =9A 102.42587
> > > GBEnr =9A =9A -1479.15727
> > >
> > > i dont understand why Electrostatic and VdW energy terms are= different. Any help will be very appreciated!!!=F1 =D7 =ED=CF=C5=CD =ED=C9= =D2=C5 - http:= //my.mail.ru/mail/nushki/> E-mail to subscribers: CHEMISTRY(!)ccl.net or use:>
> > E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net or use>
> >
> >
> >
> >
> >
> > --
> > =9A =9A =9A =9A =9A =9A =9A =9A =9A Mahmoud A. A. Ibrahim
> > =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9ACurrent Address > > =9A =9A =9A =9A =9A =9A =9A =9A =9A7.05, School of Chemistry,
> > =9A =9A =9A =9A =9A =9A =9A The University of Manchester,
> > =9A =9A =9A =9A =9AOxford Road, Manchester, M13 9PL,
> > =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9AUnited Kingdom. > >
> > =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A Home Address
> > =9A =9A =9A =9A =9A =9A =9A =9A =9A Chemistry Department,
> > =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9AFaculty of Science, > > =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A Minia University,=
> > =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9AMinia 6151= 9,
> > =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A E= gypt.
> >
> > =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9AContact Information > > =9A =9A =9A =9A =9A =9AEmail: m.ibrahim(!)compchem.net
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=9A =9A =9A= =9A =9A =9A =9A =9A =9A Mahmoud A. A. Ibrahim=9A =9A =9A =9A=9A
=9A = =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A=9A Current Address
=9A =9A =9A = =9A =9A =9A =9A =9A=9A 7.05, School of Chemistry,
=9A =9A =9A =9A =9A = =9A =9A The University of Manchester,
=9A =9A =9A =9A=9A Oxford Road, Manchester, M13 9PL,
=9A =9A =9A =9A = =9A =9A =9A =9A =9A =9A =9A=9A United Kingdom.

=9A =9A =9A =9A =9A = =9A =9A =9A =9A =9A =9A =9A Home Address
=9A =9A =9A =9A =9A =9A =9A =9A= =9A Chemistry Department,
=9A =9A =9A =9A =9A =9A =9A =9A =9A =9A=9A Fa= culty of Science,
=9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A Minia = University,
=9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A=9A Minia 61519,
=9A = =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A Egypt.

= =9A =9A =9A =9A =9A =9A =9A =9A =9A =9A=9A Contact Information
=9A =9A = =9A =9A =9A=9A Email: m.ibrahim+*+c= ompchem.net
=9A =9A =9A =9A =9A =9A =9A Website: ww= w.compchem.net
=9A =9A =9A =9A =9A =9A =9A =9A =9A=9A Fax No.: +2086= 2342601
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