From owner-chemistry@ccl.net Mon Feb 25 03:46:00 2013 From: "Georg Lefkidis lefkidis,+,physik.uni-kl.de" To: CCL Subject: CCL:G: how to define symmetry Message-Id: <-48305-130225033746-32339-IwDv8R3jC22/Vo+1+94eMg\a/server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 25 Feb 2013 09:37:35 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis ~ physik.uni-kl.de] Dear Mahnaz, besides Gaussian only works with Abelian point groups, so even if it recognizes a high symmetry group, it will most probably internally work at a lower symmetry level. Best regards George > > Sent to CCL by: Andrew Yeung [andrew.yeung###chem.tamu.edu] > Which program are you using? > > For NWChem, you can define it using the symmetry keyword. Refer to this > link: http://www.nwchem-sw.org/index.php/Geometry_examples > > I don't think it's possible to define which point group you want using > Gaussian. You can only tell Gaussian the maximum (not minimum!) symmetry > to use using symm(PG= ) keyword. Gaussian will decide if your starting > geometry has any symmetry, within certain tolerances. You can use the > symm=loose to "snap" a nearly symmetric molecule into the closest point > group. The help file is here: > http://www.gaussian.com/g_tech/g_ur/k_symmetry.htm > > > Andrew Yeung > Donald J. Darensbourg Research Group > Department of Chemistry, Texas A&M University > 3255 TAMU > College Station, TX 77843-3255 > > Tel: 979 845 4837 > Fax: 979 845 0158 > > On 2013-02-23 2:54 PM, mahnaz gh mahnaz271163!A!yahoo.com wrote: >> Sent to CCL by: "mahnaz gh" [mahnaz271163() yahoo.com] >> I'd like to enquire about how I should define a specific symmetry for my >> molecule (ligand). >> Please help me to know what is the right keyword, my symmetry is C2V. >> where should I input the keyword? >> >> mahnaz> > ------------------------------------------------------------------- Dr. Georg Lefkidis Dept. of Physics University of Kaiserslautern PO Box 3049 67653 Kaiserslautern e-mail: lefkidis(at)physik(dot)uni(dash)kl(dot)de Tel.: +49 631 205 3207 ------------------------------------------------------------------- From owner-chemistry@ccl.net Mon Feb 25 05:31:00 2013 From: "lloyd riggs lloyd.riggs_-_gmx.ch" To: CCL Subject: CCL:G: From Docking to Enzyme kinetics Message-Id: <-48306-130224070040-14282-xGtLIQT6b/Yr9gJL8XCGEg%a%server.ccl.net> X-Original-From: "lloyd riggs" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Sun, 24 Feb 2013 13:00:19 +0100 MIME-Version: 1.0 Sent to CCL by: "lloyd riggs" [lloyd.riggs]![gmx.ch] Dear Dr. Kazakiewicz,, Looking over a bunch of papers on the subject in the last 3 years for my thesis, it boils down to, good approximations can be made for small molecules, however the realistic ones other than approximations boil down to; A normal process has to be modelled into a MD system with associated solvent, and solvent make up causes large effects. A series of MDs were done over simple salt gradients from 0.015-400 mM just NaCl and KCl, and showed the affinities from the raw MDs ranged from something like 6-30 kCal/mol compared to something like 4-10 kCal/mol determined by Plasmon resonance, (raw affinities not fed into the IC50 formulas compared with Gromacs)...basically the precision of calculated affinities becomes extremely dependent on solvent, which the closer the solvent is to the conditions used to measure it the more precises the MDs work, and that seems to become complicated as not just salts, but buffers, etc can make the MD complicated, but if someone did a series of sets for common solvent buffers, etc it would become quite easy to set...as these could then be used as a standard library for personal, or uploaded larger body of people... And for other things such as proteins, the approximations stop working as they become protein specific as they do not follow similar laws as the small molecule systems...then time of simulations becomes the problem as their kinetics are in the seconds range, instead of pico or nano seconds, so a single system without applied force can take a large amount of simulation time, however they have been done and seem to fit reality from MD simulations if one has the time. Still, protein kinetics or affinities seem to fit published affinities better with less solvent effects, more temperature than small molecules (why? I assume most sims use at least simple salts, but I havn't seen much else on why?), even simple Kd, or delG with pulled, or applied force... The program in Gromacs g_lie has a paper reference to approximations which can be fed in, such as below, and works reasonably well with small molecules at least in some calculations I did at one point, both by hand using their alpha/beta correction constants, but the paper shows these are based on series of calculated affinities for small molecules, and a correction constant determined from these, and that there is a few cases these did not work possible from large amounts of hydrophobic effects (the authors assumptions), etc... So from a computer side, its limited in either the formulas you would use in say a simple calculation (ranging from 2 inputs, to inputs including solvents, protein molarity, etc...) and the more included, such as solvent, etc...the more accurate, or In a complex system, using say Gromacs or NAMD, the more the solvent reflects the reality of what you wish to measure, ie say plasma, or inter-cellular, or in vitro with salts, buffers, etc..., the more precise it would determine your desired kinetics. These simulations though represent Gaussians, and then just average, say about 10 runs, you would get very realistic measurements...or using just a g_lie, a good approximation for smaller systems if your molecules dont depend too much on hydrophobic interactions, you could also just look up the formulas from the g_lie paper and do those by hand if you have already some base things, or just the generalized formulas for IC50 from Vmax and Km, but you also have to come up with molarity corrections which arnt presented in most of the formulas for these (if you just look them up in a standard kinetic book or wiki), but they're there, in literature if you look a day,but if you have raw measurements is probably faster than simulations...hope thats not to much. The Gromacs mailing list has some of the raw calculation formulas buried in it over 8 years as well, but the included molarities, etc...you would have to change for your system, The most accurate though would be just Gromacs with your protein system, good solvent including salts, buffers or whats expected, repeated as above and calculate DelG, with each of your other molecules as well, or a quick raw approximation such as from literature...I dont know if its a project or something else though...so hope that helps, but that can take time on a large cluster... I should also say, if you have one or two known affinities from a hard calculation, such as plasmon, the others can also be done by using simple formulas, and the correction made by fitting your by hand calculations to the one you've already done empirically (do those by hand with the same calculation, the correction is the difference) which is usually a simple shift which would apply to each small molecule, but again thats simple one or two atom changes and not completely different molecules, the g_lie type method...in any case some ideas Sincerely, Stephan Watkins -------- Original-Nachricht -------- > Datum: Sat, 23 Feb 2013 11:16:38 -0500 > Von: "Denis Kazakiewicz d.kazakiewicz__gmail.com" > An: "Watkins, Steve " > Betreff: CCL: From Docking to Enzyme kinetics > > Sent to CCL by: "Denis Kazakiewicz" [d.kazakiewicz|,|gmail.com] > Hello > > The task is to calculate IC50 for different new inhibitors of enzyme with > known Vmax and Km > > Is it doable? > Which software is "better" to use? > > Best regards > Denis> > From owner-chemistry@ccl.net Mon Feb 25 06:25:00 2013 From: "Ramon Crehuet rcsqtc%iqac.csic.es" To: CCL Subject: CCL: Database of solvation energies Message-Id: <-48307-130225062015-26311-um9ozBcK9E1rKYb57GepSg]![server.ccl.net> X-Original-From: "Ramon Crehuet" Date: Mon, 25 Feb 2013 06:20:14 -0500 Sent to CCL by: "Ramon Crehuet" [rcsqtc * iqac.csic.es] Dear all, I would like to get the *experimental* solvation energy (in water) of HPO4^(2-) and HAsO4^(2-) (I want to compare with calculated values). I can deduce those from the solvation energies of H3PO4 and H3AsO4 and their pKa or from similar thermodynamic cycles. However, I looked for both sets of data and couldn't find anything! I looked at the Handbook of Chemistry and Physics, the NIST database and the Minnesota Solvation Database without success. I'm probably missing something or looking for the wrong keywords... Can anybody suggest me a database where these data are tabulated? Thanks in advance, Ramon PS. I know this is not a computational question... but it's probably a question many computational chemists have already faced! From owner-chemistry@ccl.net Mon Feb 25 08:26:00 2013 From: "Dillen, Jan jlmd]|[sun.ac.za JLMD]|[sun.ac.za" To: CCL Subject: CCL:G: how to define symmetry Message-Id: <-48308-130225004259-17443-kHKz/hCuuhajBimYrcL+Og*server.ccl.net> X-Original-From: "Dillen, Jan " Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_75B8033CA570F14DB89D5F816B3E489D2DE851EESTBEXMB02stbsun_" Date: Mon, 25 Feb 2013 05:42:43 +0000 MIME-Version: 1.0 Sent to CCL by: "Dillen, Jan [jlmd]~[sun.ac.za]" --_000_75B8033CA570F14DB89D5F816B3E489D2DE851EESTBEXMB02stbsun_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hallo Mahnaz To my knowledge, there is no keyword in Gaussian to enforce symmetry, unles= s there is an IOp that I am not aware of. If a different symmetry is report= ed than the one you think it should be, you can use the "Symm(Loose)" keywo= rd which will relax the internal criteria to determine the symmetry. There = is also an IOp to control this. If all this fails, I suggest to look at you= input coordinates again. Using a Z-matrix is very often the key to a good = starting geometry. jd ________________________________ > From: owner-chemistry+jlmd=3D=3Dsun.ac.za],[ccl.net [mailto:owner-chemistry+j= lmd=3D=3Dsun.ac.za],[ccl.net] On Behalf Of mahnaz ghiasi mahnaz271163---yahoo= .com Sent: 24 February 2013 20:50 To: Dillen, Jan Subject: CCL:G: how to define symmetry hi my program is gaussian 09, you know I'm a beginner in this field so I don't= know where should I add keywords mahnaz ________________________________ > From: "Dillen, Jan jlmd_-_sun.ac.za JLMD_-_sun.ac.za" To: "Ghiasi, Mahnaz " Sent: Sunday, February 24, 2013 8:05 PM Subject: CCL: how to define symmetry Sent to CCL by: "Dillen, Jan [jlmd:_:sun.ac.za]" It would be useful if you did specify what computer program you are using. = I tried it myself, but after about 40 years in this business, I have found = out that just shouting "help" does not work. jd -----Original Message----- > From: owner-chemistry+jlmd=3D=3Dsun.ac.za::ccl.net [mailto:owner-chemistr= y+jlmd=3D=3Dsun.ac.za::ccl.net] On Behalf Of mahnaz gh mahnaz271163!A!yahoo= .com Sent: 23 February 2013 22:55 To: Dillen, Jan Subject: CCL: how to define symmetry Sent to CCL by: "mahnaz gh" [mahnaz271163() yahoo.com] = I'd like to enquire about how I should define a specific symmetry for my mo= lecule (ligand). Please help me to know what is the right keyword, my symmetry is C2V. where should I input the keyword? mahnazhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/che= mistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt______________________= __________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en m= ag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie d= it geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hierm= ee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei o= f kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in ke= nnis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vi= r enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of d= ie oopmaak van enige l=EAers aangeheg by hierdie e-pos nie. E-mail disclaim= er This e-mail may contain confidential information and may be legally priv= ileged and is intended only for the person to whom it is addressed. If you = are not the intended recipient, you are notified that you may not use, dist= ribute or copy this document in any manner whatsoever. Kindly also notify t= he sender immediately by telephone, and delete the e-mail. The University d= oes not accept ! liability for any damage, loss or expense arising from this e-mail and/or a= ccessing any files attached to this e-mail. -=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 alsoE-mail to subscribers: CHEMISTRY]^[ccl.net or u= se:E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_75B8033CA570F14DB89D5F816B3E489D2DE851EESTBEXMB02stbsun_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hallo Mahnaz
 
To my knowledge, there is no keyw= ord in Gaussian to enforce symmetry, unless there is an IOp that I am not a= ware of. If a different symmetry is reported than the one you think it should be, you can use the "Symm(Loose)&quo= t; keyword which will relax the internal criteria to determine the symmetry= . There is also an IOp to control this. If all this fails, I suggest to loo= k at you input coordinates again. Using a Z-matrix is very often the key to a good starting geometry.<= /div>
&= nbsp;
<= span class=3D"625582605-25022013">jd

From: owner-chemistry+jlmd=3D= =3Dsun.ac.za],[ccl.net [mailto:owner-chemistry+jlmd=3D=3Dsun.ac.za],[ccl.ne= t] On Behalf Of mahnaz ghiasi mahnaz271163---yahoo.com
Sent: 24 February 2013 20:50
To: Dillen, Jan <jlmd],[sun.ac.za>
Subject: CCL:G: how to define symmetry

hi
my program is gaussian 09, you know I'm a beginner in this field so I don't= know where should I add keywords

mahnaz


From: "Dillen, Jan jlm= d_-_sun.ac.za JLMD_-_sun.ac.za" <owner-chemistry]^[ccl.net>
To: "Ghiasi, Mahnaz &q= uot; <mahnaz271163]^[yahoo.com>
Sent: Sunday, February 24, = 2013 8:05 PM
Subject: CCL: how to define= symmetry


Sent to CCL by: "Dillen, Jan [jlmd:_:sun.ac.za]" <JLMD:_:sun.a= c.za>
It would be useful if you did specify what computer program you are using. = I tried it myself, but after about 40 years in this business, I have found = out that just shouting "help" does not work.

jd

-----Original Message-----
> From: owner-chemistry+jlmd=3D=3Dsun.ac.za::ccl.net [mailto:owner-c= hemistry+jlmd=3D=3Dsun.ac.za::ccl.net] On Behalf Of mahnaz gh mahnaz271= 163!A!yahoo.com
Sent: 23 February 2013 22:55
To: Dillen, Jan <jlmd::sun.ac.za>
Subject: CCL: how to define symmetry


Sent to CCL by: "mahnaz  gh" [mahnaz271163() yahoo.com] I'd like to enquire about how I should define a specific sym= metry for my molecule (ligand).
Please help me to know what is the right keyword, my symmetry is C2V.
where should I input the keyword?

mahnazhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/che= mistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt______________________= __________

E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en m= ag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie d= it geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hierm= ee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief= die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Un= iversiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe= wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l=EAers aangeheg by hierdie e-pos nie. E-mail = disclaimer This e-mail may contain confidential information and may be lega= lly privileged and is intended only for the person to whom it is addressed.= If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in= any manner whatsoever. Kindly also notify the sender immediately by teleph= one, and delete the e-mail. The University does not accept !
liability for any damage, loss or expense arising from this e-mail and/or a= ccessing any files attached to this e-mail.



-=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
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--_000_75B8033CA570F14DB89D5F816B3E489D2DE851EESTBEXMB02stbsun_-- From owner-chemistry@ccl.net Mon Feb 25 09:01:01 2013 From: "Vignesh Kuduva Radhakrishnan krvignesh245||gmail.com" To: CCL Subject: CCL:G: Average potential difference Message-Id: <-48309-130225061926-25964-EbHVymuh/WfVbFbFLvF5IQ###server.ccl.net> X-Original-From: "Vignesh Kuduva Radhakrishnan" Date: Mon, 25 Feb 2013 06:19:25 -0500 Sent to CCL by: "Vignesh Kuduva Radhakrishnan" [krvignesh245*o*gmail.com] Dear Sir/Madam I want to know how to calculate the average potential difference for a coordination complex in gaussian 09. If anyone knows please help me. Thanks in advance. Regards, Vignesh K R Research Scholar, IITB-Monash Research Academy, IIT Bombay,Powai Mumbai-400076. From owner-chemistry@ccl.net Mon Feb 25 09:36:00 2013 From: "=?ISO-8859-1?Q?Jana_Mathauserov=E1?= jahodovykomplot__gmail.com" To: CCL Subject: CCL:G: how to define symmetry Message-Id: <-48310-130225063457-3603-KEnAhMqN32cRVzkfcOAqug(!)server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jana_Mathauserov=E1?= Content-Type: multipart/alternative; boundary=e89a8ff2514ae992f804d68aed05 Date: Mon, 25 Feb 2013 12:34:52 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jana_Mathauserov=E1?= [jahodovykomplot%gmail.com] --e89a8ff2514ae992f804d68aed05 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I am not sure what you are asking either, if you are just looking for a Gaussian input keyword, it's symm(pg=3Dc2v) for the input line. You can also 'lock' some parameters (such as angles or dihedrals etc) by adding modredundant.. J. On 23 February 2013 21:54, mahnaz gh mahnaz271163!A!yahoo.com < owner-chemistry*o*ccl.net> wrote: > > Sent to CCL by: "mahnaz gh" [mahnaz271163() yahoo.com] > I'd like to enquire about how I should define a specific symmetry for my > molecule (ligand). > Please help me to know what is the right keyword, my symmetry is C2V. > where should I input the keyword? > > mahnaz > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 --- S pozdravem Jana Mathauserov=E1 +420 606 301 164 +44 079 79 217 846 --e89a8ff2514ae992f804d68aed05 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I am not sure what you are asking either, if you are just looking for a Gau= ssian input keyword, it's symm(pg=3Dc2v)
for the input line. You can= also 'lock' some parameters (such as angles or dihedrals etc) by a= dding modredundant..

J.

On 23 February 2013 21:54, mahnaz = gh mahnaz271163!A!yahoo.com <owner-= chemistry*o*ccl.net> wrote:

Sent to CCL by: "mahnaz =A0gh" [mahnaz271163() yahoo.com]
I'd like to enquire about how I should define a specific symmetry for m= y molecule (ligand).
Please help me to know what is the right keyword, my symmetry is C2V.
where should I input the keyword?

mahnaz



-=3D This is automatically added to each message by the mailing script =3D-=
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+420 606 301 164
+44 079 79 217 846
--e89a8ff2514ae992f804d68aed05-- From owner-chemistry@ccl.net Mon Feb 25 10:11:00 2013 From: "Raphael Martinez raphaelmartinez1983###gmail.com" To: CCL Subject: CCL:G: calcfc Gaussian 09 Message-Id: <-48311-130225084910-10959-pGsd2pgpbaA3R05bgL1yXg/a\server.ccl.net> X-Original-From: "Raphael Martinez" Date: Mon, 25 Feb 2013 08:49:09 -0500 Sent to CCL by: "Raphael Martinez" [raphaelmartinez1983**gmail.com] Hello everyone: I have a very basic/quick question. I am using Gaussian 09. I know that using the option "calcfc" in the optimization is a bit expensive. So, I have few questions about it: 1. I was wondering if this option "calcfc" must be always use in the optimizations, or I can avoid it? 2. If I avoid the "calcfc", am I going to obtain a bad optimization? 3. are there certain cases in which is better to use it and cases in which I can avoid it? Thank you all for the help Raphael From owner-chemistry@ccl.net Mon Feb 25 11:31:00 2013 From: "Hanane Louanas hananelouanas#%#yahoo.fr" To: CCL Subject: CCL: the keyword SMD Message-Id: <-48312-130225101025-16006-NS2kL+OTxMDFI+qm4z+jIg_-_server.ccl.net> X-Original-From: "Hanane Louanas" Date: Mon, 25 Feb 2013 10:10:24 -0500 Sent to CCL by: "Hanane Louanas" [hananelouanas!=!yahoo.fr] Dear Sir/Madam I want to know what is the keyword "SMD" and when to use him? Thanks in advance. H.Louanas From owner-chemistry@ccl.net Mon Feb 25 12:25:00 2013 From: "Bahareh honarparvar bahareh_honarparvar:-:yahoo.com" To: CCL Subject: CCL:G: the keyword SMD Message-Id: <-48313-130225120836-25794-E/2kdxRdWHyZwKi/UaeVRg/a\server.ccl.net> X-Original-From: Bahareh honarparvar Content-Type: multipart/alternative; boundary="-113850507-1272590442-1361812110=:57931" Date: Mon, 25 Feb 2013 09:08:30 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Bahareh honarparvar [bahareh_honarparvar:+:yahoo.com] ---113850507-1272590442-1361812110=:57931 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Louanas,=0A=0ASMD is the keyword you=0Awant to use when performing a S= elf Consistent Reaction Field (SCRF) calculation=0Awith G09. This keyword w= as only made available in this last version of the=0Aprogram and it corresp= onds to Truhlar's and coworkers solvation model which is=A0recommended=A0by= =0AGaussian itself as the preferred model to calculate Delta G of solvation= .=0AThe syntax used is the=0Astandard way used in any other Gaussian input = files as follows:=0A# 'route section keywords' SCRF=3DSMD=0ASeparately, we = must=0Aeither perform a gas phase calculation or use the=A0DoVacuum keyword= =0Awithin the same=A0SCRF=A0input, and then take the energy=0Adifference be= tween gas phase and solvated models.=0A# 'route section keywords' SCRF=3D(S= MD,DoVacuum)=0AHope it helps.=0ABest regards=0ABahareh=0A=0A_______________= _________________=0A From: Hanane Louanas hananelouanas#%#yahoo.fr =0ATo: "Honarparvar, Honarparvar " =0ASent: Monday, February 25, 2013 7:10 AM=0ASubject: CCL:= the keyword SMD=0A =0A=0ASent to CCL by: "Hanane=A0 Louanas" [hananelouana= s!=3D!yahoo.fr]=0ADear Sir/Madam=0A=0AI want to know what is the keyword "S= MD" and when to use him? =0A=0AThanks in advance.=0AH.Louanas=0A=0A=0A=0A-= =3D This is automatically added to each message by the mailing script =3D-= =0A= =0A=0Aloo= k up the X-Original-From: line in the mail header.=0A=0AE-mail to subscribe= rs: CHEMISTRY/a\ccl.net or use:=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/= send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST/a\ccl.net o= r use=0A=A0 =A0 =A0=0A=0ASu= bscribe/Unsubscribe: =0A=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.= shtml=0A=0A=0A=0AJob:= http://www.ccl.net/jobs =0AConferences: http://server.ccl.net/chemistry/an= nouncements/conferences/=0A=0ASearch Messages: http://www.ccl.net/chemistry= /searchccl/index.shtml=0A=0AIf your mail bounces from CCL with 5.7.1 error,= check:=0A=A0 =A0 =A0=0A=0ARTFI: http://www= .ccl.net/chemistry/aboutccl/instructions/ ---113850507-1272590442-1361812110=:57931 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Louanas,

=0A=0A
SMD is the keyword you=0Awant = to use when performing a Self Consistent Reaction Field (SCRF) calculation= =0Awith G09. This keyword was only made available in this last version of t= he=0Aprogram and it corresponds to Truhlar's and coworkers solvation model = which is recommended by=0AGaussian itself as the preferred model = to calculate Delta G of solvation.
=0A=0A
= The syntax used is the=0Ast= andard way used in any other Gaussian input files as follows:
=0A=0A
# 'route section keywords' = SCRF=3DSMD
=0A=0A
Separately, we must=0Aeither perform a= gas phase calculation or use the DoVacuum keyword=0Awithin the= same SCRF input, and then take the energy=0Adifference be= tween gas phase and solvated models.
=0A=0A
# 'route section keywords' SCRF=3D(SMD,DoVacuum)
Hope it helps.=
=0A=0A
Best regards
Baha= reh
From:<= /span> Hanane Louanas hananelouanas#%#yahoo.fr <owner-chemistry/a\ccl.= net>
To: "Honarparv= ar, Honarparvar " <bahareh_honarparvar/a\yahoo.com>
Sent: Monday, February 25, 2013 = 7:10 AM
Subject: CCL: = the keyword SMD

=0A
Sent to CCL by: "Hanane = Louanas" [hananelouanas!=3D!yahoo.fr]
Dear Sir/Madam

I want to k= now what is the keyword "SMD" and when to use him?

Thanks in advanc= e.
H.Louanas



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---113850507-1272590442-1361812110=:57931-- From owner-chemistry@ccl.net Mon Feb 25 15:10:01 2013 From: "John McKelvey jmmckel^-^gmail.com" To: CCL Subject: CCL:G: how to define symmetry Message-Id: <-48314-130225113024-9609-yde+LqUW4EARJUR++3r4yg^server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 25 Feb 2013 11:30:17 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel .. gmail.com] In the utility NEWZMAT I believe there is an option to set the looseness to be used in symmetry determination for a new input file. John McKelvey On Mon, Feb 25, 2013 at 12:42 AM, Dillen, Jan jlmd]|[sun.ac.za JLMD]|[sun.ac.za wrote: > Hallo Mahnaz > > To my knowledge, there is no keyword in Gaussian to enforce symmetry, unless there is an IOp that I am not aware of. If a different symmetry is reported than the one you think it should be, you can use the "Symm(Loose)" keyword which will relax the internal criteria to determine the symmetry. There is also an IOp to control this. If all this fails, I suggest to look at you input coordinates again. Using a Z-matrix is very often the key to a good starting geometry. > > jd > > ________________________________ >> From: owner-chemistry+jlmd==sun.ac.za:-:ccl.net [mailto:owner-chemistry+jlmd==sun.ac.za:-:ccl.net] On Behalf Of mahnaz ghiasi mahnaz271163---yahoo.com > Sent: 24 February 2013 20:50 > To: Dillen, Jan > Subject: CCL:G: how to define symmetry > > hi > my program is gaussian 09, you know I'm a beginner in this field so I don't know where should I add keywords > > mahnaz > > > ________________________________ >> From: "Dillen, Jan jlmd_-_sun.ac.za JLMD_-_sun.ac.za" > To: "Ghiasi, Mahnaz " > Sent: Sunday, February 24, 2013 8:05 PM > Subject: CCL: how to define symmetry > > > Sent to CCL by: "Dillen, Jan [jlmd:_:sun.ac.za]" > It would be useful if you did specify what computer program you are using. I tried it myself, but after about 40 years in this business, I have found out that just shouting "help" does not work. > > jd > > -----Original Message----- >> From: owner-chemistry+jlmd==sun.ac.za::ccl.net [mailto:owner-chemistry+jlmd==sun.ac.za::ccl.net] On Behalf Of mahnaz gh mahnaz271163!A!yahoo.com > Sent: 23 February 2013 22:55 > To: Dillen, Jan > Subject: CCL: how to define symmetry > > > Sent to CCL by: "mahnaz gh" [mahnaz271163() yahoo.com] I'd like to enquire about how I should define a specific symmetry for my molecule (ligand). > Please help me to know what is the right keyword, my symmetry is C2V. > where should I input the keyword? > > mahnazhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt________________________________ > > E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige lêers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept ! > liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.the strange characters on the top line to the ]^[ sign. You can alsoE-mail to subscribers: CHEMISTRY]^[ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_75B8033CA570F14DB89D5F816B3E489D2DE851EESTBEXMB02stbsun_ > Content-Type: text/html; charset"iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > > > > > > > >
Hallo Mahnaz
>
 
>
To my knowledge, there is no keyword in Gaussian to enforce symmetry, unless there is an IOp that I am not aware of. If a different symmetry is reported > than the one you think it should be, you can use the "Symm(Loose)" keyword which will relax the internal criteria to determine the symmetry. There is also an IOp to control this. If all this fails, I suggest to look at you input coordinates again. Using a > Z-matrix is very often the key to a good starting geometry.
>
 
>
jd
>
>
>
> From: owner-chemistry+jlmd==sun.ac.za:-:ccl.net [mailto:owner-chemistry+jlmd==sun.ac.za:-:ccl.net] > On Behalf Of mahnaz ghiasi mahnaz271163---yahoo.com
> Sent: 24 February 2013 20:50
> To: Dillen, Jan <jlmd:-:sun.ac.za>
> Subject: CCL:G: how to define symmetry
>
>
>
>
> hi
> my program is gaussian 09, you know I'm a beginner in this field so I don't know where should I add keywords
>
> mahnaz
>

>
>

>
>
>
>
>
> From: "Dillen, Jan jlmd_-_sun.ac.za JLMD_-_sun.ac.za" <owner-chemistry]^[ccl.net>
> To: "Ghiasi, Mahnaz " <mahnaz271163]^[yahoo.com> >
> Sent: Sunday, February 24, 2013 8:05 PM
> Subject: CCL: how to define symmetry
>
>
>
> Sent to CCL by: "Dillen, Jan [jlmd:_:sun.ac.za]" <JLMD:_:sun.ac.za>
> It would be useful if you did specify what computer program you are using. I tried it myself, but after about 40 years in this business, I have found out that just shouting "help" does not work.
>
> jd
>
> -----Original Message-----
> > From: owner-chemistry+jlmd==sun.ac.za::ccl.net [mailto:owner-chemistry+jlmd==sun.ac.za::ccl.net] On Behalf Of mahnaz gh mahnaz271163!A!yahoo.com
> Sent: 23 February 2013 22:55
> To: Dillen, Jan <jlmd::sun.ac.za>
> Subject: CCL: how to define symmetry
>
>
> Sent to CCL by: "mahnaz  gh" [mahnaz271163() > yahoo.com] I'd like to enquire about how I should define a specific symmetry for my molecule (ligand).
> Please help me to know what is the right keyword, my symmetry is C2V.
> where should I input the keyword?
>
> mahnazhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt________________________________
>
> E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie > dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos > en/of die oopmaak van enige lêers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, > you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept !
> liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.
>
>
> > the strange characters on the top line to the ]^[ sign. You can also >
> E-mail to subscribers: > CHEMISTRY]^[ccl.net or use:
>      
>
> E-mail to administrators: > CHEMISTRY-REQUEST]^[ccl.net or use
>       http://www.ccl.net/cgi-bin/ccl/send_ccl_message
>      
> > > > >      
> >
>
>
>
>
>
>
> > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel/a\gmail.com From owner-chemistry@ccl.net Mon Feb 25 16:44:01 2013 From: "Denis Kazakiewicz d.kazakiewicz]*[gmail.com" To: CCL Subject: CCL:G: From Docking to Enzyme kinetics Message-Id: <-48315-130225164318-22934-P8QXhCfBbiO9EnZx88pY0A===server.ccl.net> X-Original-From: Denis Kazakiewicz Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 25 Feb 2013 22:43:07 +0100 MIME-Version: 1.0 Sent to CCL by: Denis Kazakiewicz [d.kazakiewicz_+_gmail.com] Great Thank you very much indeed for comprehensive answer On 24.02.2013 13:00, lloyd riggs lloyd.riggs_-_gmx.ch wrote: > Sent to CCL by: "lloyd riggs" [lloyd.riggs]![gmx.ch] > Dear Dr. Kazakiewicz,, > > Looking over a bunch of papers on the subject in the last 3 years for my thesis, it boils down to, good approximations can be made for small molecules, however the realistic ones other than approximations boil down to; > > A normal process has to be modelled into a MD system with associated solvent, and solvent make up causes large effects. A series of MDs were done over simple salt gradients from 0.015-400 mM just NaCl and KCl, and showed the affinities from the raw MDs ranged from something like 6-30 kCal/mol compared to something like 4-10 kCal/mol determined by Plasmon resonance, (raw affinities not fed into the IC50 formulas compared with Gromacs)...basically the precision of calculated affinities becomes extremely dependent on solvent, which the closer the solvent is to the conditions used to measure it the more precises the MDs work, and that seems to become complicated as not just salts, but buffers, etc can make the MD complicated, but if someone did a series of sets for common solvent buffers, etc it would become quite easy to set...as these could then be used as a standard library for personal, or uploaded larger body of people... > > And for other things such as proteins, the approximations stop working as they become protein specific as they do not follow similar laws as the small molecule systems...then time of simulations becomes the problem as their kinetics are in the seconds range, instead of pico or nano seconds, so a single system without applied force can take a large amount of simulation time, however they have been done and seem to fit reality from MD simulations if one has the time. Still, protein kinetics or affinities seem to fit published affinities better with less solvent effects, more temperature than small molecules (why? I assume most sims use at least simple salts, but I havn't seen much else on why?), even simple Kd, or delG with pulled, or applied force... > > The program in Gromacs g_lie has a paper reference to approximations which can be fed in, such as below, and works reasonably well with small molecules at least in some calculations I did at one point, both by hand using their alpha/beta correction constants, but the paper shows these are based on series of calculated affinities for small molecules, and a correction constant determined from these, and that there is a few cases these did not work possible from large amounts of hydrophobic effects (the authors assumptions), etc... > > So from a computer side, its limited in either the formulas you would use in say a simple calculation (ranging from 2 inputs, to inputs including solvents, protein molarity, etc...) and the more included, such as solvent, etc...the more accurate, or > > In a complex system, using say Gromacs or NAMD, the more the solvent reflects the reality of what you wish to measure, ie say plasma, or inter-cellular, or in vitro with salts, buffers, etc..., the more precise it would determine your desired kinetics. These simulations though represent Gaussians, and then just average, say about 10 runs, you would get very realistic measurements...or using just a g_lie, a good approximation for smaller systems if your molecules dont depend too much on hydrophobic interactions, you could also just look up the formulas from the g_lie paper and do those by hand if you have already some base things, or just the generalized formulas for IC50 from Vmax and Km, but you also have to come up with molarity corrections which arnt presented in most of the formulas for these (if you just look them up in a standard kinetic book or wiki), but they're there, in literature if you look a day,but if you have raw measurements is probably faster than simulatio! > ns...hope thats not to much. The Gromacs mailing list has some of the raw calculation formulas buried in it over 8 years as well, but the included molarities, etc...you would have to change for your system, > > The most accurate though would be just Gromacs with your protein system, good solvent including salts, buffers or whats expected, repeated as above and calculate DelG, with each of your other molecules as well, or a quick raw approximation such as from literature...I dont know if its a project or something else though...so hope that helps, but that can take time on a large cluster... > > I should also say, if you have one or two known affinities from a hard calculation, such as plasmon, the others can also be done by using simple formulas, and the correction made by fitting your by hand calculations to the one you've already done empirically (do those by hand with the same calculation, the correction is the difference) which is usually a simple shift which would apply to each small molecule, but again thats simple one or two atom changes and not completely different molecules, the g_lie type method...in any case some ideas > > Sincerely, > > Stephan Watkins > > -------- Original-Nachricht -------- >> Datum: Sat, 23 Feb 2013 11:16:38 -0500 >> Von: "Denis Kazakiewicz d.kazakiewicz__gmail.com" >> An: "Watkins, Steve " >> Betreff: CCL: From Docking to Enzyme kinetics >> Sent to CCL by: "Denis Kazakiewicz" [d.kazakiewicz|,|gmail.com] >> Hello >> >> The task is to calculate IC50 for different new inhibitors of enzyme with >> known Vmax and Km >> >> Is it doable? >> Which software is "better" to use? >> >> Best regards >> Denis> >