From owner-chemistry@ccl.net Tue Mar 5 00:11:00 2013 From: "David Gallagher gallagher.da[*]gmail.com" To: CCL Subject: CCL: High Accuracy Transition States Message-Id: <-48385-130304173640-19450-EbHVymuh/WfVbFbFLvF5IQ[#]server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="------------040708050905060400050701" Date: Mon, 04 Mar 2013 14:36:33 -0800 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da---gmail.com] This is a multi-part message in MIME format. --------------040708050905060400050701 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Bill, Not sure if this is of interest, but the latest version of MOPAC2012 has a new approach to calculating transition state energies. Reaction barrier heights have been parameterized using published coupled cluster high-level/ab initio/calculations on the PM7 transition state and related ground state geometries (reactants and products). It is fairly new so there is little published yet on how it performs against other methods. However, it should be relatively very fast and inexpensive to compare it with your available data. See http://www.cacheresearch.com/mopac.html Cheers, David On 3/4/2013 4:52 AM, Laidig, Bill laidig.wd^^pg.com wrote: > Sent to CCL by: "Laidig, Bill" [laidig.wd-,-pg.com] > All, > > I have been using thermodynamic recipe methods like G3(MP2) to get good estimates for reaction thermodynamics. Does anyone know if there are any analogous "activation barrier" recipe methods? I tried searching for this but have not found anything. > > Thanks, > Bill > --------------040708050905060400050701 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Bill,

Not sure if this is of interest, but the latest version of MOPAC2012 has a new approach to calculating transition state energies.  Reaction barrier heights have been parameterized using published coupled cluster high-level ab initio calculations on the PM7 transition state and related ground state geometries (reactants and products).  It is fairly new so there is little published yet on how it performs against other methods.  However, it should be relatively very fast and inexpensive to compare it with your available data.  See http://www.cacheresearch.com/mopac.html

Cheers,
David


On 3/4/2013 4:52 AM, Laidig, Bill laidig.wd^^pg.com wrote:
Sent to CCL by: "Laidig, Bill" [laidig.wd-,-pg.com]
All,

I have been using thermodynamic recipe methods like G3(MP2) to get good estimates for reaction thermodynamics.  Does anyone know if there are any analogous "activation barrier" recipe methods?  I tried searching for this but have not found anything.

Thanks,
Bill

--------------040708050905060400050701-- From owner-chemistry@ccl.net Tue Mar 5 03:01:00 2013 From: "Bahareh honarparvar bahareh_honarparvar_._yahoo.com" To: CCL Subject: CCL:G: the keyword SMD Message-Id: <-48386-130305025230-23097-Tb3yxJhXmiDvgMcwwE9yPw(-)server.ccl.net> X-Original-From: Bahareh honarparvar Content-Type: multipart/alternative; boundary="1024699347-170388628-1362469944=:56662" Date: Mon, 4 Mar 2013 23:52:24 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Bahareh honarparvar [bahareh_honarparvar]^[yahoo.com] --1024699347-170388628-1362469944=:56662 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Wenli,=0Awe don't do just SCRF=3DSMD single point calculation without = FREQ!=0Aso in rout section of Gaussian program we should do freq calculatio= n the on optimized=0Astructure in solvent and SMD solvation model.=0AFirst = do freq calculation in gas as # Method/basis set =A0 =A0freq=3Dnoraman =A0= =0Aand get the G value in gas.=0ASecond,do freq calculation in solvent with= SMD keyword as=0A# Method/basis set =A0 =A0freq=3Dnoraman =A0scrf=3D(solve= nt=3Dwater,smd)=0Aand get the G value in solvent.=0Adelta G is =3DG value i= n solent -=A0G value in gas=0A=0AAbout temperature,the default for=A0temper= ature in=A0Gaussian program is 298 K,however,you can change it.=0A=0AHope i= t helps=0ABahareh=0A=0A=0A________________________________=0A From: Zork Zo= u zorkzou!A!gmail.com =0ATo: "Honarparvar, Honarpa= rvar " =0ASent: Monday, March 4, 20= 13 11:05 AM=0ASubject: CCL:G: the keyword SMD=0A =0A=0ADear Bahareh, Delta = G depends on temperature. If we do just SCRF=3DSMD single point calculation= without FREQ, is this correct? Thanks. Wenli=0A=0AOn Mon, Feb 25, 2013 at = 11:08 AM, Bahareh honarparvar bahareh_honarparvar:-:yahoo.com wrote:=0A=0ADear Louanas,=0A>=0A>=0A>SMD is the keyword you= =0Awant to use when performing a Self Consistent Reaction Field (SCRF) calc= ulation=0Awith G09. This keyword was only made available in this last versi= on of the=0Aprogram and it corresponds to Truhlar's and coworkers solvation= model which is=A0recommended=A0by=0AGaussian itself as the preferred model= to calculate Delta G of solvation.=0A>The syntax used is the=0Astandard wa= y used in any other Gaussian input files as follows:=0A># 'route section ke= ywords' SCRF=3DSMD=0A>Separately, we must=0Aeither perform a gas phase calc= ulation or use the=A0DoVacuum keyword=0Awithin the same=A0SCRF=A0input, and= then take the energy=0Adifference between gas phase and solvated models.= =0A># 'route section keywords' SCRF=3D(SMD,DoVacuum)=0A>Hope it helps.=0A>B= est regards=0A>Bahareh --1024699347-170388628-1362469944=:56662 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable 
Dear Wenli=
,
we don't do just SCRF=3DSMD single point calculation w=
ithout FREQ!
so in rout section of Gaussian program we sh=
ould do freq calculation the on optimized
 structure in =
solvent and SMD solvation model.
First do freq calculati=
on in gas as # Method/basis set    freq=3Dnoraman  
and get the G value in gas.
Second,<=
/span>do freq calculation in solvent with SMD keyword as
# Method/basis set    freq=3Dnoraman &nb= sp;scrf=3D(solvent=3Dwater,smd)
and get the G value=
 in solvent.
delta G is =3DG value in solent= - G value in gas

About temperature,the default for temperature= in Gaussian program is= 298 K,however,you can change it.

Hope it helps
Bahareh

= From: Zork Zou zorkzou!A!g= mail.com <owner-chemistry{}ccl.net>
To: "Honarparvar, Honarparvar " <bahareh_hona= rparvar{}yahoo.com>
Sent: Monday, March 4, 2013 11:05 AM
Subject: CCL:G: the keyword SMD

=0A<= div id=3D"yiv835636065">
Dear Bahareh,=0A=0ADelta G d=
epends on temperature. If we do just SCRF=3DSMD single point calculation wi=
thout FREQ, is this correct? Thanks.=0A=0AWenli

On Mon, Feb 25, 2013 at 11:08 AM, Bahareh hona= rparvar bahareh_honarparvar:-:yahoo.com <owner-chemistry() ccl.net> wro= te:
=0A
Dear Louanas,
=0A

=0A=0A=0A
SMD is the keyw= ord you=0Awant to use when performing a Self Consistent Reaction Field (SCR= F) calculation=0Awith G09. This keyword was only made available in this las= t version of the=0Aprogram and it corresponds to Truhlar's and coworkers so= lvation model which is recommended by=0AGaussian itself as the pr= eferred model to calculate Delta G of solvation.
=0A=0A
The syntax used is the=0Astandard wa= y used in any other Gaussian input files as follows:=0A=0A
<= span style=3D""># 'route section keywords' SCRF=3DSMD<= /span>
=0A=0A
Separately= , we must=0Aeither perform a gas phase calculation or use the DoVac= uum keyword=0Awithin the same SCRF input, and then tak= e the energy=0Adifference between gas phase and solvated models.<= /u>
=0A=0A
# 'route section keywords' SCRF=3D(SMD,D= oVacuum)
=0A
<= span style=3D"">Hope it helps.
=0A=0A
Best regards
Bahareh
=0A

--1024699347-170388628-1362469944=:56662-- From owner-chemistry@ccl.net Tue Mar 5 04:35:01 2013 From: "John Simmie john.simmie-x-nuigalway.ie" To: CCL Subject: CCL: Hi-accuract transition states Message-Id: <-48387-130305043352-9807-1mQ8f5oIc1MwnUwh+a3Igg_-_server.ccl.net> X-Original-From: "John Simmie" Date: Tue, 5 Mar 2013 04:33:51 -0500 Sent to CCL by: "John Simmie" [john.simmie^_^nuigalway.ie] >Sent to CCL by: "Laidig, Bill" [laidig.wd-,-pg.com] All, > >I have been using thermodynamic recipe methods like G3(MP2) to get good >estimates for reaction thermodynamics. Does anyone know if there are any >analogous "activation barrier" recipe methods? I tried searching for this >but have not found anything It would not be a good idea IMHO to use a different level of theory for TSs to that that you have used already for reactans and products. So stick with G3(MP2) or else re-do reactants, TSs & products at a better level... what that better level is depends on your system, computational expense, etc. John Simmie//john.simmie%%nuigalway.ie//C3, NUI Galway, Ireland From owner-chemistry@ccl.net Tue Mar 5 08:43:00 2013 From: "Jeya vimalan jeyavimalan2k---gmail.com" To: CCL Subject: CCL: Standardization of a crystal structure Message-Id: <-48388-130305052120-29435-As/FOBGnOJQ9jqxGeD/meg],[server.ccl.net> X-Original-From: Jeya vimalan Content-Type: multipart/alternative; boundary=14dae9340e5b2c9d6204d72ad5d6 Date: Tue, 5 Mar 2013 11:21:11 +0100 MIME-Version: 1.0 Sent to CCL by: Jeya vimalan [jeyavimalan2k##gmail.com] --14dae9340e5b2c9d6204d72ad5d6 Content-Type: text/plain; charset=ISO-8859-1 Dear Colleagues, Could any one explain, what is meant by standardization of a crystal structure. Can it be used directly on the crystal structures obtained from experiments. (without changing the original information) Also, please suggest any free wares that can do this. best regards, jeya --14dae9340e5b2c9d6204d72ad5d6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear=A0Colleagues,

Could any one explain, what is meant<= /div>
by standardization of a crystal structure.

Can it be used directly on the crystal structures
obtained fro= m experiments. (without changing the original information)

Also, please suggest any free wares that can
= do this.

best regards,
jeya
--14dae9340e5b2c9d6204d72ad5d6-- From owner-chemistry@ccl.net Tue Mar 5 10:12:00 2013 From: "Errol Lewars elewars-$-trentu.ca" To: CCL Subject: CCL: High Accuracy Transition States Message-Id: <-48389-130305101037-31223-fjDmGjwIwIqwH0UKaeFDTg .. server.ccl.net> X-Original-From: Errol Lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 05 Mar 2013 10:11:15 -0500 MIME-Version: 1.0 Sent to CCL by: Errol Lewars [elewars%trentu.ca] 2013 March 05 "thermodynamic recipe methods", "'activation barrier' recipe methods": For practical and accurate (1.5 kcal mol-1, 6.3 kJ mol-1) calculations you might look at B. J. Lynch, D. G. Truhlar, J Phys Chem A, 2001, 105, 2936-2941. Regarding kinetics in contrast to thermodynamics, of course energy difference (barrier height) alone is not sufficient for calculaton of a rate constant--you also need the preexponential factor. E. Lewars == Laidig, Bill laidig.wd^^pg.com wrote: > Sent to CCL by: "Laidig, Bill" [laidig.wd-,-pg.com] > All, > > I have been using thermodynamic recipe methods like G3(MP2) to get good estimates for reaction thermodynamics. Does anyone know if there are any analogous "activation barrier" recipe methods? I tried searching for this but have not found anything. > > Thanks, > Bill> > From owner-chemistry@ccl.net Tue Mar 5 12:08:01 2013 From: "Andrew Voronkov drugdesign###yandex.ru" To: CCL Subject: CCL: docking programs, which account for T-shaped pi-pi interactions Message-Id: <-48390-130305091131-7704-4skGL+qcXTiWB/6PPj0oCw|server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=koi8-r Date: Tue, 05 Mar 2013 18:11:20 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign-*-yandex.ru] The binding site is quite flexible. But I have X-ray structure of this ligand with protein with T-shaped stacking and it is not reproduced correctly (I ve used GoldSuite). Best regards, Andrew 28.01.2013, 21:30, "John W Liebeschuetz john!^!ccdc.cam.ac.uk" : > Sent to CCL by: "John W Liebeschuetz" [john,+,ccdc.cam.ac.uk] > Dear Andrew, > šššššššššWhilst it is true that most docking scoring functions do not take account of T stacking pi-pi interactions as well as they do hydrogen bonding interactions, there may be another reason why your original docking did not give the experimental result. šHave you investigated whether there is some movement of the protein in the more recent structure, that facilitates this T-stacking of šaromatic groups? > > šššššššššIf so, including very accurate descriptions of T stacking in the docking algorithm may not be sufficient to get a good binding pose, when using your original protein model. Conversely a more general scoring function might reproduce the correct pose in the most recent protein model. > > ššššššššššššššššššššššššššRegards > > ššššššššššššššššššššššššššššššššššššJohn > > Dr John W. Liebeschuetz > Life Sciences Research & Applications Manager > Cambridge Crystallographic Data Centre > 12 Union Rd., Cambridge CB2 1EZ, UK> ššššššhttp://www.ccl.net/cgi-bin/ccl/send_ccl_message> ššššššhttp://www.ccl.net/cgi-bin/ccl/send_ccl_message> ššššššhttp://www.ccl.net/chemistry/sub_unsub.shtml> ššššššhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Mar 5 12:45:00 2013 From: "Jacco van de Streek jacco.vandestreek::sund.ku.dk" To: CCL Subject: CCL: Standardization of a crystal structure Message-Id: <-48391-130305124425-9752-mJnfRCF6sIefoWrGDEdrMQ~~server.ccl.net> X-Original-From: Jacco van de Streek Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Mar 2013 17:44:12 +0000 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [jacco.vandestreek/a\sund.ku.dk] > Could any one explain, what is meant > by standardization of a crystal structure. What is probably meant is the standardisation of the unit-cell parameters and the space group. Crystallographers have a set of conventions (i.e. rules that are not based on any physics) regarding what a standard set of unit-cell parameters should look like. For example, if the unit-cell lengths a, b and c are equivalent by (but not related by) symmetry, some conventions state that the unit-cell parameters should be labeled such that ab>c, as with all arbitrary conventions, they are a matter of taste). For unit cells with two angles identical to 90 degrees based on the space-group symmetry, the convention is that the remaining angle should be called beta (or gamma according to some other conventions). Space-group symmetry can also be standardised. For space group number 14, the standard setting is P 1 21/c 1 with the inversion at the origin, for example. Most standardisation also includes the atomic coordinates: it is convenient if the atomic coordinates are reported in such a manner that they form a connected molecule without the need to apply the space-group symmetry (including translations) to generate symmetry-related copies, and the fractional coordinates of the centre of mass of the molecule should all be in the range [0, 1> (perhaps even in the range [0,1/2> or whatever, depending on the space-group symmetry). Also the number of atoms that should be reported is usually standardised to be restricted to the smallest set required to reconstruct the entire crystal structure (by applying the space-group symmetry). The standardisation may also include the atom labeling itself. > Can it be used directly on the crystal structures > obtained from experiments. (without changing the original information) In principle, yes. In practice, some programs may either change the number of decimals (because they choose to save all files with a fixed number of decimal places, ignoring the input) and your coordinates may either gain some meaningless trailing zeros or lose some semi-meaningful fourth or fifth decimal, and some programs may omit the estimated standard deviations on the atomic coordinates, or even on the unit-cell parameters. When you want to do an energy minimisation anyway, this should not make any difference, as these estimated standard deviations do not affect the final result anyway. > Also, please suggest any free wares that can > do this. WinGX: http://www.chem.gla.ac.uk/~louis/software/wingx/ Platon: http://www.cryst.chem.uu.nl/spek/ Best wishes, -- Dr Jacco van de Streek Department of Pharmacy University of Copenhagen