From owner-chemistry@ccl.net Mon Jan 10 03:07:00 2011 From: "Markus Kaukonen markus.kaukonen]*[iki.fi" To: CCL Subject: CCL: Software for ring size and other distributions? Message-Id: <-43583-110110015952-17730-rDZ+NNnoYQUAirXSZG9J9w-.-server.ccl.net> X-Original-From: Markus Kaukonen Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 10 Jan 2011 08:59:41 +0200 MIME-Version: 1.0 Sent to CCL by: Markus Kaukonen [markus.kaukonen{=}iki.fi] Dear CCL, Is there (free) software to analyse ring size, number of neighbours, and other distributions in amorphous materials? Terveisin, Markus -- --www=http://www.iki.fi/markus.kaukonen --Markus.Kaukonen##iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) --- From owner-chemistry@ccl.net Mon Jan 10 04:19:01 2011 From: "Gabriele Cruciani gabri(0)chemiome.chm.unipg.it" To: CCL Subject: CCL: Pioglitazone Tautomers Message-Id: <-43584-110110041639-29911-psMgBoIupoJh4Rqybl692g^^^server.ccl.net> X-Original-From: Gabriele Cruciani Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 10 Jan 2011 10:16:23 +0100 MIME-Version: 1.0 Sent to CCL by: Gabriele Cruciani [gabri##chemiome.chm.unipg.it] Nancy, the first form you reported is the most stable in water at pH 7.0. However, the fact that one form is more stable than another in water does not help you to understand which form will be more 'relevant' for docking. In protein the tautomeric equilibria may produce and stabilize different forms according to the complementary site. There are examples of tautomeric form in protein not stable in water, where the energy difference is more than 5 Kcal/mol. MoKa software (www.moldiscovery.com) is fast and accurate to produce tautomer stable in water, but it can produce also all the (plausible) tautomeric forms. Then, a possibility is to dock them into your protein, to see if docking methods may differentiate their binding. Gabriele Cruciani > Hi All, > > I am performing molecular docking and molecular dynamics simulations of the > thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein > (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous different > tautomeric states; I have attached a figure depicting several of them. > Which tautomer would be dominant at the physiological pH of ~7.0? > > Also, are there any software programs that can predict which tautomer would > be correct? > > Thanks in advance, > Nancy > From owner-chemistry@ccl.net Mon Jan 10 04:53:00 2011 From: "Vincent Leroux vincent.leroux^^^loria.fr" To: CCL Subject: CCL: Pioglitazone Tautomers Message-Id: <-43585-110110041918-32367-aEJC+mbUW9k7vs77Lx2EcA|*|server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 10 Jan 2011 10:19:04 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux^loria.fr] Hi Nancy, I suppose you did docking and MD with explicit hydrogens - should be the case. So you did several calculations, one for each tautomeric state. Inspect the docking and MD results. The charge model is approximate, but is there any significant difference in the scores (docking) / protein-ligand and ligand-solvent interaction energies (MD) due to the tautomeric state already? Inspect the structures, especially if there are such differences: is the formation of a stable protein-ligand H-bond depending of the changing protonation state of a given atom? If so, you would favor the corresponding state(s). Secondarily, is your "variable" ligand group bound in a highly polar pocket? If so you might want to compute optimized charges then perform some MM/PBSA minimization from docking results to get a better idea of what could happen. Only after such investigations should you decide which of the remaining ligand state is the most relevant at pH 7, using tools specialized to do such predictions. Do not be tempted to select one state without looking at docking/MD results first. If your only parameter for selecting a state is the pH, you assume that going from bulk solvent to the binding site environment will have no influence... Do not forget the histidines, if there are some on the binding site... choosing their protonation state is a similar story. Look after H-bonds forming upon ligand binding, and if the picture is the same regardless the protonation state, then you can simply thrust the H++ server for example. Regards VL Le 10/01/11 00:09, Nancy nancy5villa]^[gmail.com a écrit : > Hi All, > > I am performing molecular docking and molecular dynamics simulations of > the thiazolidinedione pioglitazone binding to the PPAR-gamma receptor > protein (PDB ID: 1ZGY). The thiazolidinedione ring can exist in > numerous different tautomeric states; I have attached a figure depicting > several of them. Which tautomer would be dominant at the physiological > pH of ~7.0? > > Also, are there any software programs that can predict which tautomer > would be correct? > > Thanks in advance, > Nancy > > From owner-chemistry@ccl.net Mon Jan 10 08:13:01 2011 From: "veera pandian ponnuchamy veera.pandi33[a]gmail.com" To: CCL Subject: CCL:G: How to calculate Hyperpolarizability using G03 Message-Id: <-43586-110110055233-9632-gDBwKSJ/+K4BQaT3ehQnYg{=}server.ccl.net> X-Original-From: "veera pandian ponnuchamy" Date: Mon, 10 Jan 2011 05:52:32 -0500 Sent to CCL by: "veera pandian ponnuchamy" [veera.pandi33(_)gmail.com] I am a beginner in computational chemistry doing my M.Sc project on prediction of hyperpolarizability of organic molecule using Gaussian 03/09. When I use polar=enonly in the route section, the program completed successfully. I dont know which value I have to take from the output to get the hyperpolarizability? Whether my keyword is right or wrong? Any suggestions will be helpful Thanks in advance. By Veerpandian.P From owner-chemistry@ccl.net Mon Jan 10 08:48:00 2011 From: "Piotr Nowak omenthegreat|a|gmail.com" To: CCL Subject: CCL:G: Gaussian: IOp(1/40) and saddle point optimization Message-Id: <-43587-110109210306-26617-v+EhYrnItyNRa4bBgdWFlg!A!server.ccl.net> X-Original-From: Piotr Nowak Content-Type: multipart/alternative; boundary=0022152d5f71b0df650499745d52 Date: Mon, 10 Jan 2011 03:02:53 +0100 MIME-Version: 1.0 Sent to CCL by: Piotr Nowak [omenthegreat!^!gmail.com] --0022152d5f71b0df650499745d52 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL users, According to http://www.gaussian.com/g_tech/g_iops/ov1.htm#1-40 one can recalculate the Hessian every N optimization steps - IOp(1/40=N). Unfortunately this seems to be completely ignored when combined with transition state optimization because "opt(calcfc/calcall)" keyword is still necessary and overrides IOp setting. Does anyone know how to solve this problem? Best regards, PN -- Piotr Nowak PhD student University of Groningen Stratingh Institute for Chemistry Nijenborgh 4 9747 AG Groningen The Netherlands http://www.google.com/profiles/omenthegreat --0022152d5f71b0df650499745d52 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL users,

According to=A0http://www.gaussian.com/g_tech/g_iops/ov1.htm#1-40<= /a>=A0one can recalculate the Hessian every N optimization steps - IOp(1/40= =3DN). Unfortunately this seems to be completely ignored when combined with= transition state optimization because "opt(calcfc/calcall)" keyw= ord is still necessary and overrides IOp setting. Does anyone know how to s= olve this problem?

Best regards,
PN

--
Piotr Nowak --0022152d5f71b0df650499745d52-- From owner-chemistry@ccl.net Mon Jan 10 09:24:00 2011 From: "Vladimir Chupakhin chupvl:-:gmail.com" To: CCL Subject: CCL: Pioglitazone Tautomers Message-Id: <-43588-110110034039-25075-XfYdgoBpfZJQ4jQwg2HDpA],[server.ccl.net> X-Original-From: Vladimir Chupakhin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Mon, 10 Jan 2011 11:40:04 +0300 MIME-Version: 1.0 Sent to CCL by: Vladimir Chupakhin [chupvl]*[gmail.com] Deaк Nancy, try ChemAxon pKa prediction online http://www.chemaxon.com/marvin/sketch/index.php you can also try other software vendors, but I suggest you to dock all of the tautomers and correlate energy of binding or scoring function with activity. -- Vladimir Chupakhin, Postdoc at joint project between Chemoinformatics laboratory and Structural Chemogenomics group University of Strasbourg, Strasbourg, France On Mon, Jan 10, 2011 at 2:09 AM, Nancy nancy5villa]^[gmail.com wrote: > Hi All, > > I am performing molecular docking and molecular dynamics simulations of the > thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein > (PDB ID: 1ZGY).  The thiazolidinedione ring can exist in numerous different > tautomeric states; I have attached a figure depicting several of them. > Which tautomer would be dominant at the physiological pH of ~7.0? > > Also, are there any software programs that can predict which tautomer would > be correct? > > Thanks in advance, > Nancy > > > From owner-chemistry@ccl.net Mon Jan 10 09:59:01 2011 From: "Krishna Govender kk.govender:_:gmail.com" To: CCL Subject: CCL: MOPAC users Message-Id: <-43589-110110011407-10551-4zD1IvDnHVA7hXWtGT4Xhw : server.ccl.net> X-Original-From: Krishna Govender Content-Type: multipart/alternative; boundary=90e6ba5bbaf763cb00049977df42 Date: Mon, 10 Jan 2011 08:13:54 +0200 MIME-Version: 1.0 Sent to CCL by: Krishna Govender [kk.govender()gmail.com] --90e6ba5bbaf763cb00049977df42 Content-Type: text/plain; charset=ISO-8859-1 You can setup MOPAC input files with Avogadro. It is a free software package which you can obtain from: http://avogadro.openmolecules.net/wiki/Main_Page On Sun, Jan 9, 2011 at 10:37 PM, Olawale Lukman Olasunkanmi waleolasunkanmi ~ gmail.com wrote: > > Sent to CCL by: "Olawale Lukman Olasunkanmi" [waleolasunkanmi|,|gmail.com] > Dear all, > I appreciate your earlier contributions while I was getting started. > Please, how do I correct the following errors emanating from or stopping my > calculations: > 1. the gradient norm is too high for force field calculations > 2. the gradient norm is too high, results may be inaccurate > Can you suggest a molecular builder that I can readily download and use to > generate my input file? > Thank you in anticipation of your responses.> > > -- Regards K. K. Govender BSc (Hons)(Chemistry), MSc (Chemistry) University of Pretoria PhD Graduate Student Scientific Computing Research Unit University of Cape Town 082-930-4098 021-650-2530 Email: kk.govender-*-gmail.com krishna.govender-*-uct.ac.za --90e6ba5bbaf763cb00049977df42 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
You can setup MOPAC input files with Avogadro.
It is a free software package which you can obtain from: http://avogadro.openmolecul= es.net/wiki/Main_Page

On Sun, Jan 9, 2011 at 10:37 PM, Olawale Lukman = Olasunkanmi waleolasunkanmi ~ gmail.com <owner-chemis= try-*-ccl.net> wrote:

Sent to CCL by: "Olawal= e Lukman Olasunkanmi" [waleolasunkanmi|,|gmail.com]
Dear all,
I appreciate your earlier contributions while I was getting st= arted.
Please, how do I correct the following errors emanating from or s= topping my calculations:
1. the gradient norm is too high for force fiel= d calculations
2. the gradient norm is too high, results may be inaccurate
Can you sugg= est a molecular builder that I can readily download and use to generate my = input file?
Thank you in anticipation of your responses.



-=3D This is automatically added to each message by the mailing script = =3D-
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--
Regards
K.= K. Govender
BSc (Hons)(Chemistry), MSc (Chemistry)
University of Pretoria
PhD Gra= duate Student
Scientific Computing Research Unit
University of Cape = Town
082-930-4098
021-650-2530
Email: kk.govender-*-gmail.com
krishna.govender-*-uct.ac.za
--90e6ba5bbaf763cb00049977df42-- From owner-chemistry@ccl.net Mon Jan 10 10:33:00 2011 From: "Deskins, N Aaron nadeskins++WPI.EDU" To: CCL Subject: CCL: Force field calculations-getting started Message-Id: <-43590-110110092932-29444-fCiHbvz5e6DiYC1IRTpWYQ-$-server.ccl.net> X-Original-From: "Deskins, N Aaron" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_B8C68B7EDCF1FC458F0604C0F8E45D65050C4660S197adminwpiedu_" Date: Mon, 10 Jan 2011 09:29:16 -0500 MIME-Version: 1.0 Sent to CCL by: "Deskins, N Aaron" [nadeskins[*]WPI.EDU] --_000_B8C68B7EDCF1FC458F0604C0F8E45D65050C4660S197adminwpiedu_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hello fellow CCL'ers, I find myself increasingly in need of running some force field calculatio= ns (e.g. OPLS) for organic/biological molecules, and am looking for the bes= t way to get started. I come from an electronic structure background where = making an input file is pretty straight-forward. Choose atomic coordinates = (xyz), basis set, methodology, and run the calculation. Setting up an input file for the various molecular mechanics methods howe= ver seems more complicated. You can start with the xyz atomic coordinates, = but you also have to worry about various atom types for the same element, a= tom connectivity, etc. Can anyone suggest some software/website/tutorial that would help in settin= g up an input file? I'm leaning towards using DL_POLY (I have experience with this code for= 'simpler' systems) with the OPLS force field, but this isn't set in stone.= OPLS seems to be widely used for the types of molecules I'm interested in = (organics). Thank you, N. Aaron Deskins Assistant Professor Chemical Engineering Department Worcester Polytechnic Institute Worcester, MA http://users.wpi.edu/~nadeskins --_000_B8C68B7EDCF1FC458F0604C0F8E45D65050C4660S197adminwpiedu_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello fellow CCL’ers,

 

  I find myself increasingly in need of= running some force field calculations (e.g. OPLS) for organic/biological m= olecules, and am looking for the best way to get started. I come from an el= ectronic structure background where making an input file is pretty straight= -forward. Choose atomic coordinates (xyz), basis set, methodology, and run = the calculation.

 

  Settin= g up an input file for the various molecular mechanics methods however seem= s more complicated. You can start with the xyz atomic coordinates, but you = also have to worry about various atom types for the same element, atom conn= ectivity, etc.

 

Can anyone suggest s= ome software/website/tutorial that would help in setting up an input file?<= o:p>

 

    I’m leaning= towards using DL_POLY (I have experience with this code for ‘simpler= ’ systems) with the OPLS force field, but this isn’t set in sto= ne. OPLS seems to be widely used for the types of molecules I’m inter= ested in (organics).

 

Thank you,&nb= sp;

 

N. Aa= ron Deskins

Assistant Professor

Chemical Engineering Department

Worcester Polytechnic Institute

Worcester, MA

http://users.= wpi.edu/~nadeskins

 

=

 

= --_000_B8C68B7EDCF1FC458F0604C0F8E45D65050C4660S197adminwpiedu_-- From owner-chemistry@ccl.net Mon Jan 10 11:08:00 2011 From: "Decai Yu decaiyu23]^[yahoo.com" To: CCL Subject: CCL:G: eliminate Spin Contamination for CCSD and MP2 in Gaussian Message-Id: <-43591-110109084506-24760-z5416we8AKZrGd2PVZhJXA!=!server.ccl.net> X-Original-From: Decai Yu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sun, 9 Jan 2011 05:44:54 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Decai Yu [decaiyu23]![yahoo.com] Dave, Thanks. But how about CCSD? Are there any way to get CCSD energies without spin contamination? Decai --- On Sat, 1/8/11, Close, David M. CLOSEDa/mail.etsu.edu wrote: > From: Close, David M. CLOSEDa/mail.etsu.edu > Subject: CCL:G: eliminate Spin Contamination for CCSD and MP2 in Gaussian > To: "Yu, Decai " > Date: Saturday, January 8, 2011, 9:56 AM > > Sent to CCL by: "Close, David M." [CLOSED-x-mail.etsu.edu] > Yu: >   In the output there is the normal MP2 energy and > then a PMP2 energy, followed by three values of S2. > The first value of S2 is greater than 1?  That's from > the normal MP2 run.  But the next value of S2 comes > from the projected MP2 run, and this should be somewhat > closer to 0.75.  Is it? >   Regards, Dave Close > > -----Original Message----- > > From: owner-chemistry+closed==etsu.edu^_^ccl.net > [mailto:owner-chemistry+closed==etsu.edu^_^ccl.net] On > Behalf Of Decai Yu decaiyu23:-:yahoo.com > Sent: Friday, January 07, 2011 6:44 PM > To: Close, David M. > Subject: CCL:G: eliminate Spin Contamination for CCSD and > MP2 in Gaussian > > > Sent to CCL by: Decai Yu [decaiyu23,yahoo.com] > Dear All, > > I have encountered significant spin-contamination with > MP2 > and CCSD using Gaussian 09. > Can anyone comment on how to eliminate the spin > contamination using Gaussian? > > Your help is appreciated. > > Regards, > > Decai Yuhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > > > -= This is automatically added to each message by the > mailing script =- > To recover the email address of the author of the message, > please change > 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 >      >      >      > > > From owner-chemistry@ccl.net Mon Jan 10 13:50:00 2011 From: "Alex Allardyce aa[-]chemaxon.com" To: CCL Subject: CCL: Pioglitazone Tautomers Message-Id: <-43592-110110120613-29405-VbnhnGc0j8wzZqoCpsrDvA^^^server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------090101080907040201060003" Date: Mon, 10 Jan 2011 18:05:57 +0100 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa[*]chemaxon.com] This is a multi-part message in MIME format. --------------090101080907040201060003 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit Hi Nancy, Another way to try the ChemAxon pKa/tautomers etc. To see others you can draw, paste structure or paste name or smiles (or open a file for a single molecule) from the index page and press on "Calculate properties". Once there you can select the tautomers (and conformers) boxes to view (this will be remembered next time). On one hand you can see a wealth of discovery related data (try "Open All" in "Manage Calculations" tab) but cannot (yet) parametrize calculations for pH, micro/macro, temp, etc, tho chemicalize will give graph data over the pH range for pKa. However MarvinSketch online will let you tune the parameters and give numerical output as well as SDF. Looking at the images you attached - it seems you have MarvinSketch already - see the tools menu for these calculators. If you are in academic research see this link for info and signup for our free academic package Cheers Alex On 1/10/2011 9:40 AM, Vladimir Chupakhin chupvl:-:gmail.com wrote: > Sent to CCL by: Vladimir Chupakhin [chupvl]*[gmail.com] > Deaк Nancy, > try ChemAxon pKa prediction online > http://www.chemaxon.com/marvin/sketch/index.php > you can also try other software vendors, but I suggest you to dock all > of the tautomers and correlate energy of binding or scoring function > with activity. > -- *Alex Allardyce* Marketing Dir. *ChemAxon**Ltd*. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Tel: +361 453 0435 Fax: +361 4532659 mailto:aa- -chemaxon.com --------------090101080907040201060003 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit Hi Nancy,

Another way to try the ChemAxon pKa/tautomers etc. To see others you can draw, paste structure or paste name or smiles (or open a file for a single molecule) from the index page and press on "Calculate properties". Once there you can select the tautomers (and conformers) boxes to view (this will be remembered next time).

On one hand you can see a wealth of discovery related data (try "Open All" in "Manage Calculations" tab) but cannot (yet) parametrize calculations for pH, micro/macro, temp, etc, tho chemicalize will give graph data over the pH range for pKa. However MarvinSketch online will let you tune the parameters and give numerical output as well as SDF.

Looking at the images you attached - it seems you have MarvinSketch already - see the tools menu for these calculators. If you are in academic research see this link for info and signup for our free academic package

Cheers
Alex
On 1/10/2011 9:40 AM, Vladimir Chupakhin chupvl:-:gmail.com wrote: 
Sent to CCL by: Vladimir Chupakhin [chupvl]*[gmail.com]
Deaк Nancy,
try ChemAxon pKa prediction online
http://www.chemaxon.com/marvin/sketch/index.php
you can also try other software vendors, but I suggest you to dock all
of the tautomers and correlate energy of binding or scoring function
with activity.

--
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037 Hungary
http://www.chemaxon.com
Tel: +361 453 0435
Fax: +361 4532659
mailto:aa- -chemaxon.com
--------------090101080907040201060003-- From owner-chemistry@ccl.net Mon Jan 10 15:26:00 2011 From: "Victor Rosas Garcia rosas.victor__gmail.com" To: CCL Subject: CCL: MOPAC users Message-Id: <-43593-110110112420-26250-zzDIj9zYjFmIxcV1uY6b2Q+*+server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=0015174c1098b94f5604998065e4 Date: Mon, 10 Jan 2011 10:24:08 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor+*+gmail.com] --0015174c1098b94f5604998065e4 Content-Type: text/plain; charset=ISO-8859-1 To specify the gradient, use GNORM=0.01, check the manual http://www.openmopac.net/manual/index.html Both Ghemical and Avogadro are easy-to-use molecular builders, and both will export to mopac format. Most likely, you will have to be able to open the resulting file in a text editor to do some minor adjustments. Ghemical will only export the geometry, and you will need to add the keywords by hand. The GUI in Avogadro allows you to set the values of the most common keywords but not all of them. Ghemical: http://www.uku.fi/~thassine/projects/ghemical/ Avogadro: http://avogadro.openmolecules.net/wiki/Main_Page Hope this helps Victor 2011/1/9 Olawale Lukman Olasunkanmi waleolasunkanmi ~ gmail.com < owner-chemistry(_)ccl.net> > > Sent to CCL by: "Olawale Lukman Olasunkanmi" [waleolasunkanmi|,|gmail.com] > Dear all, > I appreciate your earlier contributions while I was getting started. > Please, how do I correct the following errors emanating from or stopping my > calculations: > 1. the gradient norm is too high for force field calculations > 2. the gradient norm is too high, results may be inaccurate > Can you suggest a molecular builder that I can readily download and use to > generate my input file? > Thank you in anticipation of your responses. > > > --0015174c1098b94f5604998065e4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable To specify the gradient, use GNORM=3D0.01, check the manual http://www.openmopac.net/manual/ind= ex.html

Both Ghemical and Avogadro are easy-to-use molecular bui= lders, and both will export to mopac format.=A0 Most likely, you will have = to be able to open the resulting file in a text editor to do some minor adj= ustments.=A0 Ghemical will only export the geometry, and you will need to a= dd the keywords by hand.=A0 The GUI in Avogadro allows you to set the value= s of the most common keywords but not all of them.

Ghemical: ht= tp://www.uku.fi/~thassine/projects/ghemical/
Avogadro: http://avogadro.openmolecul= es.net/wiki/Main_Page

Hope this=A0 helps

Victor

2011= /1/9 Olawale Lukman Olasunkanmi waleolasunkanmi ~ gmail.com <owner-chemistry(_)ccl.net>

Sent to CCL by: "Olawale Lukman Olasunkanmi" [waleolasunkanmi|,|<= a href=3D"http://gmail.com" target=3D"_blank">gmail.com]
Dear all,
I appreciate your earlier contributions while I was getting started.
Please, how do I correct the following errors emanating from or stopping my= calculations:
1. the gradient norm is too high for force field calculations
2. the gradient norm is too high, results may be inaccurate
Can you suggest a molecular builder that I can readily download and use to = generate my input file?
Thank you in anticipation of your responses.


--0015174c1098b94f5604998065e4-- From owner-chemistry@ccl.net Mon Jan 10 16:20:00 2011 From: "Nancy nancy5villa]-[gmail.com" To: CCL Subject: CCL: Pioglitazone Tautomers Message-Id: <-43594-110110145148-15882-mK/nlsIcw0zsd3wF3EGYFA^-^server.ccl.net> X-Original-From: Nancy Content-Type: multipart/alternative; boundary=20cf3054a61978e1d504998349b5 Date: Mon, 10 Jan 2011 14:50:59 -0500 MIME-Version: 1.0 Sent to CCL by: Nancy [nancy5villa{}gmail.com] --20cf3054a61978e1d504998349b5 Content-Type: text/plain; charset=ISO-8859-1 How do you know that the first tautomer (diketone) is the most stable at pH 7.0? Thanks, Nancy On Mon, Jan 10, 2011 at 4:16 AM, Gabriele Cruciani gabri(0) chemiome.chm.unipg.it wrote: > > Sent to CCL by: Gabriele Cruciani [gabri##chemiome.chm.unipg.it] > Nancy, > the first form you reported is the most stable in water at pH 7.0. > However, the fact that one form is more stable than another in water does > not help you to understand which form will be more 'relevant' for docking. > In protein the tautomeric equilibria may produce and stabilize different > forms according to the complementary site. There are examples of tautomeric > form in protein not stable in water, where the energy difference is more > than 5 Kcal/mol. > > MoKa software (www.moldiscovery.com) is fast and accurate to produce > tautomer stable in water, but it can produce also all the (plausible) > tautomeric forms. > > Then, a possibility is to dock them into your protein, to see if docking > methods may differentiate their binding. > > Gabriele Cruciani > > > > > Hi All, >> >> I am performing molecular docking and molecular dynamics simulations of >> the >> thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein >> (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous >> different >> tautomeric states; I have attached a figure depicting several of them. >> Which tautomer would be dominant at the physiological pH of ~7.0? >> >> Also, are there any software programs that can predict which tautomer >> would >> be correct? >> >> Thanks in advance, >> Nancyhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --20cf3054a61978e1d504998349b5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable How do you know that the first tautomer (diketone) is the most stable at pH= 7.0?

Thanks,
Nancy



On = Mon, Jan 10, 2011 at 4:16 AM, Gabriele Cruciani gabri(0)chemiome.chm.unipg.it <owner-chemistry[]ccl.net> wrote:

Sent to CCL by: Gabriele Cruciani [gabri##chemiome.chm.unipg.it]
Nancy,
the first form you reported is the most stable in water at pH 7.0.
However, the fact that one form is more stable than another in water does n= ot help you to understand which form will be more 'relevant' for do= cking. In protein the tautomeric equilibria may produce and stabilize diffe= rent forms according to the complementary site. There are examples of tauto= meric form in protein not stable in water, where the energy difference is m= ore than 5 Kcal/mol.

MoKa software (ww= w.moldiscovery.com) is fast and accurate to produce tautomer stable in = water, but it can produce also all the (plausible) tautomeric forms.

Then, a possibility is to dock them into your protein, to see if docking me= thods may differentiate their binding.

Gabriele Cruciani




Hi All,

I am performing molecular docking and molecular dynamics simulations of the=
thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein (PDB ID: 1ZGY). =A0The thiazolidinedione ring can exist in numerous differe= nt
tautomeric states; I have attached a figure depicting several of them.
Which tautomer would be dominant at the physiological pH of ~7.0?

Also, are there any software programs that can predict which tautomer would=
be correct?

Thanks in advance,
Nancy




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--20cf3054a61978e1d504998349b5-- From owner-chemistry@ccl.net Mon Jan 10 22:17:00 2011 From: "Simon Halstead joyjoyhappyjoy,+,yahoo.co.uk" To: CCL Subject: CCL: Force field calculations-getting started Message-Id: <-43595-110110204529-14792-x+6Rmy6ORdbaFLdSqYo6OQ_-_server.ccl.net> X-Original-From: Simon Halstead Content-Type: multipart/alternative; boundary="0-489931461-1294710316=:76772" Date: Tue, 11 Jan 2011 01:45:16 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Simon Halstead [joyjoyhappyjoy\a/yahoo.co.uk] --0-489931461-1294710316=:76772 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi,=0A=0ADL_POLY comes with a GUI that should be able to write FIELD files.= The program =0Aalso comes with some test files to you familiarise yourself= with the various =0Aoptions with a bit of help from the manual. For creati= ng larger systems, I =0Ausually write a short fortran program that can writ= e suitable FIELD and CONFIG =0Afiles for a series of compounds. It saves a = lot of time and potential human =0Aerror.=0AFinally, there is a dedicated d= l_poly forum which may be of use to you=0Ahttp://www.cse.scitech.ac.uk/disc= o/forums/ubbthreads.php?Cat=3D0=0A=0ARegards,=0A=0ASimon Halstead=0A=0A=0A= =0A=0A________________________________=0AFrom: "Deskins, N Aaron nadeskins+= +WPI.EDU" =0ATo: "Halstead, Simon " =0ASent: Mon, January 10, 2011 10:29:16 PM=0ASubject:= CCL: Force field calculations-getting started=0A=0A=0AHello fellow CCL=E2= =80=99ers,=0A =0A I find myself increasingly in need of running some forc= e field calculations =0A(e.g. OPLS) for organic/biological molecules, and a= m looking for the best way to =0Aget started. I come from an electronic str= ucture background where making an =0Ainput file is pretty straight-forward.= Choose atomic coordinates (xyz), basis =0Aset, methodology, and run the ca= lculation. =0A=0A =0A Setting up an input file for the various molecular m= echanics methods however =0Aseems more complicated. You can start with the = xyz atomic coordinates, but you =0Aalso have to worry about various atom ty= pes for the same element, atom =0Aconnectivity, etc.=0A =0ACan anyone sugge= st some software/website/tutorial that would help in setting up =0Aan input= file?=0A =0A I=E2=80=99m leaning towards using DL_POLY (I have experien= ce with this code for =0A=E2=80=98simpler=E2=80=99 systems) with the OPLS f= orce field, but this isn=E2=80=99t set in stone. OPLS =0Aseems to be widely= used for the types of molecules I=E2=80=99m interested in (organics). =0A= =0A =0AThank you, =0A =0AN. Aaron Deskins=0AAssistant Professor=0AChemical= Engineering Department=0AWorcester Polytechnic Institute=0AWorcester, MA= =0Ahttp://users.wpi.edu/~nadeskins=0A=0A=0A --0-489931461-1294710316=:76772 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi,

DL_POLY comes with a GUI that should be able t= o write FIELD files. The program also comes with some test files to you fam= iliarise yourself with the various options with a bit of help from the manu= al. For creating larger systems, I usually write a short fortran program th= at can write suitable FIELD and CONFIG files for a series of compounds. It = saves a lot of time and potential human error.
Finally, there is a dedic= ated dl_poly forum which may be of use to you
= http://www.cse.scitech.ac.uk/disco/forums/ubbthreads.php?Cat=3D0=

Regards,

Simon Halstead

From: "Deskins, N Aaron nadeskins++WPI.EDU" <o= wner-chemistry-*-ccl.net>
To: "Halstead, Simon " <joyjoyhappyjoy-*-yahoo.co.uk>
Sent: Mon, January 10, 2011 = 10:29:16 PM
Subject: CC= L: Force field calculations-getting started

=0A
Hi Aaro= n,
 
You may want to look at D= L_FIELD which is a new utility for constructing the FIELD file for use in D= L_POLY. It is free of charge and only requires registration.
 
An alternative is to= use the AMBER "antechamber" program to determine the atom t= ypes, count (and list) bounds between the atoms (and harmonic for= ce constants between them,) angles and harmonic angle bend harmonic force constants, dihedrals (proper and improper) along with the related pa= rameters, etc. according to the AMBER force field functions. Parameter= s for many types of potential (including OPLS) are available in A= MBER. Once you get the list of bonds, angles, dihedrals from the antechamber program, it is a much easier task to prepare the DL_P= OLY FIELD file. I can send a more detailed description of the procedur= e if you have access to AMBER and antechamber.
 
I hope this helps.=
 
Best regards,
Saman Alavi
 
From: owner-chemistry+saman.ala= vi=3D=3Dnrc.ca:_:ccl.net [owner-chemistry+saman.alavi=3D=3Dnrc.ca:_:ccl.net= ] On Behalf Of Deskins, N Aaron nadeskins++WPI.EDU [owner-chemistry= :_:ccl.net]
Sent: January-10-11 9:29 AM
To: Alavi, Saman
Subject: CCL: Force field calculations-getting started

He= llo fellow CCL=92ers,

&n= bsp;

&n= bsp; I find myself increasingly in need of running some force field ca= lculations (e.g. OPLS) for organic/biological molecules, and am looking for= the best way to get started. I come from an electronic structure background where making an input file is pretty straight-forward= . Choose atomic coordinates (xyz), basis set, methodology, and run the calc= ulation.

 

&n= bsp; Setting up an input file for the various molecular mechanics meth= ods however seems more complicated. You can start with the xyz atomic coord= inates, but you also have to worry about various atom types for the same element, atom connectivity, etc.

 

Ca= n anyone suggest some software/website/tutorial that would help in setting = up an input file?

 

&n= bsp;   I=92m leaning towards using DL_POLY (I have experience wit= h this code for =91simpler=92 systems) with the OPLS force field, but this = isn=92t set in stone. OPLS seems to be widely used for the types of molecules I=92m interested in (organics).

 

Th= ank you, 

 

N. Aaron Deskins

Assistant Professor

Chemical Engineering Department

Worcester Polytechnic Institute

Worcester, MA

http://users.wpi.edu/~nadeskins

 

 

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