From owner-chemistry@ccl.net Fri Aug 8 01:59:00 2008 From: "Frank Neese neese+*+thch.uni-bonn.de" To: CCL Subject: CCL: Computational Chemistry software Message-Id: <-37518-080808015814-17140-ev2HMXo8REvZ2fFoe0GeTw:server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 08 Aug 2008 07:57:55 +0200 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese**thch.uni-bonn.de] Dear CCLers, just briefly following up on John McKelvey's message to this list. Yes, i think that ORCA is probably a good and user friendly choice for what Arun is looking for (except for the MM part). However, in order to stop any speculations of this kind: there is no code sharing whatsoever between TurboMole (a Fortran program) and ORCA (a C++ program). These are completely independent projects. Best regards, FN ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ John McKelvey jmmckel]![gmail.com wrote: > ORCA is an extremely good free program for academics containing both > semi-empirical [INDO/S, MNDO, AM1, PM3, and I think the only pure > STO-based NDDO method that follows Pople's original intent and also > has analytical derivatives,] as well as _many_ DFT and TDDFT > methodologies, and shares many aspects with the very good commercial > code TURBOMOLE (there is a lot of code sharing between them). It has > very good support, and of course has binaries available in many > flavors of hardware/OS for (I think for MAC), Windows, and Linux (AMD > and Intel) and I think some 32 and 64 bit versions. > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Dear All, I am looking for a free computational Chemistry software(s) which works in Windows operating systems which can do simple ab initio calculations as well as molecular mechanics. This will be used primarily as a teaching tool for 2nd and 3rd year undergraduate students. Additionally, software which can display orbitals etc will also be useful as a teaching tool. Any recommendations on choice of software for teaching or pointers towards any free software will be deeply appreciated. Thanks, Arun Dr. Arun Venkatnathan Assistant Professor, Chemistry Indian Institute of Science Education and Research Pune India. 411021 Tel: 91-20-2590-8044 From owner-chemistry@ccl.net Fri Aug 8 09:05:00 2008 From: "Mudit k Dixit dixitmuditk^^gmail.com" To: CCL Subject: CCL: Hydrogen Storage Message-Id: <-37519-080808015143-3350-B+j1FtkIGhX3cjhaUGldng{=}server.ccl.net> X-Original-From: "Mudit k Dixit" Date: Fri, 8 Aug 2008 01:51:39 -0400 Sent to CCL by: "Mudit k Dixit" [dixitmuditk * gmail.com] what are the pakages I can use to study Hydrogen storage materials. thanks mudit From owner-chemistry@ccl.net Fri Aug 8 09:40:00 2008 From: "Mudit Dixit dixitmuditk%gmail.com" To: CCL Subject: CCL: Computational Chemistry software Message-Id: <-37520-080808072623-22306-i8jMrYjTsk0+0klqhf6rpA~!~server.ccl.net> X-Original-From: "Mudit Dixit" Date: Fri, 8 Aug 2008 07:26:19 -0400 Sent to CCL by: "Mudit Dixit" [dixitmuditk_._gmail.com] The program ORCA is a modern electronic structure program package with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to correlated ab initio methods. It can also treat environmental and relativistic effects. You can get this by following link http://www.redbrick.dcu.ie/~noel/linux4chemistry/linux4chemistry.py MUDIT DIXIT JRF NATIONAL CHEMICAL LABORATORY(NCL) INDIA From owner-chemistry@ccl.net Fri Aug 8 10:15:00 2008 From: "Simon Halstead shalstead(a)hit.edu.cn" To: CCL Subject: CCL: Ab initio on bridged rings Message-Id: <-37521-080807214545-1766-3FRcnFRPqRi+DtYSc45Xhg:_:server.ccl.net> X-Original-From: Simon Halstead Content-Type: text/plain; charset=us-ascii Date: Fri, 8 Aug 2008 01:45:27 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Simon Halstead [shalstead:hit.edu.cn] Dear all, Thanks for the replies. First of all, I did perform an initial calculation on the structures at pm3 level. The calculations were quick and located the stationary point. Here are the coordinates for one of the structures: 22 C 0.3278408383 0.2556632257 -0.6958480605 C -0.6749330239 -0.8804489119 -0.6637892896 C -1.9925684835 -0.1640159207 -0.9990405167 C -1.7766055437 0.8451058680 0.2241238684 C -0.4411950377 1.4743937219 -0.1151303166 C -1.5534544981 -0.1580831322 1.3412477527 C -0.8667997706 -1.1855423421 0.8239710266 C 1.7051382469 -0.0777886638 -0.1199445501 C 2.6193671392 1.0431733002 0.3616649580 O 2.0929414634 -1.2296044956 -0.1029624608 H -2.8775370468 -0.7968676192 -0.8864627204 H -1.9667233161 0.3565767738 -1.9434479163 H -1.7811465980 0.0168100327 2.3851269590 H -0.4303225256 -2.0227098365 1.3505314534 H -2.6065279205 1.5190592093 0.3872605483 H -0.4083901218 -1.7381098498 -1.2646540978 H -0.5730139012 2.2617625045 -0.8428063319 H 0.0092293900 1.8939641578 0.7693408676 H 0.5599560611 0.4970449650 -1.7524902275 H 3.5406839415 0.6093501882 0.7475333961 H 2.8549606891 1.7285215964 -0.4508702454 H 2.1443540827 1.6275360285 1.1469846166 Thanks again for your help, Simon Halstead ----- Original Message ---- > From: errol lewars elewars+*+trentu.ca To: "Halstead, Simon " Sent: Wednesday, August 6, 2008 4:25:25 AM Subject: CCL: Ab initio on bridged rings Sent to CCL by: errol lewars [elewars||trentu.ca] 2008 August 05 Could you give us the structure (cartesians) of one (preferably the smallest) of your troublesome conmpounds)? E. Lewars ============= Simon Halstead shalstead . hit.edu.cn wrote: >Sent to CCL by: "Simon Halstead" [shalstead:hit.edu.cn] > >Dear all, > >I am trying to optimize some bridged (1-4) cyclohexane rings. I initially optimized them using sempiempirical methods. These calculations converged very rapidly. However, I then tried to optimize the resulting structures at a higher level of theory. These high level calculations have failed to converge, despite being run for a large number of steps. I have tried HF, MP2 and B3LYP with a variety of basis sets but nothing appears to converge. Visualizing the outputs of the failed calculations shows no problems with the structure. >Does anyone have any experience with structures like this or can anyone give me a suggestion of how best to optimize bridged rings? >I am using GAMESS if this makes any differnce. > >Thanks for your help, > >Simon Halsteadhttp://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 Fri Aug 8 14:30:02 2008 From: "Radoslaw Kaminski rkaminski.rk%%gmail.com" To: CCL Subject: CCL:G: Crysallographic structure Vs optimized Message-Id: <-37522-080808105258-8819-1eylyLt+3Bdx8NrluE8rkw(!)server.ccl.net> X-Original-From: "Radoslaw Kaminski" Content-Type: multipart/alternative; boundary="----=_Part_43288_28815050.1218203842967" Date: Fri, 8 Aug 2008 15:57:22 +0200 MIME-Version: 1.0 Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk() gmail.com] ------=_Part_43288_28815050.1218203842967 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, For fixing any value in Gaussian 03 it is also possible to write in the command line Opt=Z-matrix and than after the block of variables you simply put block of constants. For example for H2O molecule. # HF/STO-3G Opt=Z-matrix water 0 1 H O 1 d1 H 2 d2 1 a2 d1 0.9 d2 0.9 a2 104.5 In the case of above the d1 and d2 are variables and a2 is constant and it won't be changes during the optimization process. Of course to use that method you have to have your molecule written as z-matrix in appropriate way. If you want to use the method mentioned by Hemant Kumar Srivastava you need to use, as I remember (I hope correctly), the word POpt (partial optymalization) instead of Opt. And now concerning your question. Remember that in crystal you have a lot of intermolecular interactions. They can change a molecular structure a little bit. The crystal structure is ALWAYS only the starting point in calculations. The question is that IR and UV spectra were measured in crystal or in solution? If, for example, in solution, the average structure can be as calculated, it means planar, and that could be the reason why experimental values fit to theoretical ones. I didn't see your molecule but the possible reason could be also that you have some intramolecular interactions which cannot be "caught" by B3LYP method with such small base (6-31G*), you can also try different functionals or bigger basis sets (e.g. Dunning ones). Remember also that more restrains and constrains you use in calculations you will be farther from real minimum. Try and calculate the frequencies in your partially optimized structure, you will probably find some negative ones. If I may also comment that you applied symmetry. Why? If the molecule is small enough and during the optimization it "catches" reasonable geometry in my opinion you don't need to use symmetry restrains. I also hope that this comment help a little bit:) Best wishes Radek Kaminski 1) Warsaw University of Technology, Department of Chemistry 2) Warsaw University, Department of Chemistry, Division of Crystallography 2008/8/7 Hemant Srivastava hemantkrsri%gmail.com > > Sent to CCL by: "Hemant Srivastava" [hemantkrsri+*+gmail.com] > Dear Shabbir, > > For fixing diahedral angle you can write following in input file al last. > D 1 2 3 4 F > where 1 2 3 4 are atom numbers. > > For the other problem you have I think you should try different > method/basis or solvent calculation. > > Hope it will help. > > Hemant Kumar Srivastava, > The Hebrew University of Jerusalem > =================================== > > > On 8/6/08, Mr shabbir shabbir*_*nenu.edu.cn > wrote: > > > > Sent to CCL by: "Mr shabbir" [shabbir__nenu.edu.cn] > > Hello CCL users! > > I am a in some confusion want to explain it. Please If some one have an > idea let me know also. > > I have taken a crystallographic structure and optimized it using > Gaussian03 with C2 symmetry and b3lyp/6-31G* method. After optimization it > gave me a round about planer structure. After this I have calculated its UV > and IR spectra that is in good agreement with experimental values but the > crystallographic structure has a dihedral angle 40 degree with side pyrrol > rings which is not in my optimized structure. So can I say that my Gassphase > optimized structure is reliable on the basis of calculated experimental > values and start my futher calculations? Secondly I tried to freeze that > dihedral angle using guessview but it could not freeze during optimization. > How to freeze dihedral angle during optimization so that it will not change > during calculations? > > Mr.Shabbir > > Northeast normal university Changchun > > P.R.China > > shabbir++nenu.edu.cn> > > ------=_Part_43288_28815050.1218203842967 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Hi,

For fixing any value in Gaussian 03 it is also = possible to write in the command line Opt=3DZ-matrix and than after the blo= ck of variables you simply put block of constants. For example for H2O mole= cule.

# HF/STO-3G Opt=3DZ-matrix

water

0 1
H
O 1 d1
H = 2 d2 1 a2

d1 0.9
d2 0.9

a2 104.5

In the case of abo= ve the d1 and d2 are variables and a2 is constant and it won't be chang= es during the optimization process. Of course to use that method you have t= o have your molecule written as z-matrix in appropriate way. If you want to= use the method mentioned by=20 Hemant Kumar Srivastava you need to use, as I remember (I hope correctly), = the word POpt (partial optymalization) instead of Opt.

And now conce= rning your question. Remember that in crystal you have a lot of intermolecu= lar interactions. They can change a molecular structure a little bit. The c= rystal structure is ALWAYS only the starting point in calculations. The que= stion is that IR and UV spectra were measured in crystal or in solution? If= , for example, in solution, the average structure can be as calculated, it = means planar, and that could be the reason why experimental values fit to t= heoretical ones. I didn't see your molecule but the possible reason cou= ld be also that you have some intramolecular interactions which cannot be &= quot;caught" by B3LYP method with such small base (6-31G*), you can al= so try different functionals or bigger basis sets (e.g. Dunning ones). Reme= mber also that more restrains and constrains you use in calculations you wi= ll be farther from real minimum. Try and calculate the frequencies in your = partially optimized structure, you will probably find some negative ones. I= f I may also comment that you applied symmetry. Why? If the molecule is sma= ll enough and during the optimization it "catches" reasonable geo= metry in my opinion you don't need to use symmetry restrains.

I also hope that this comment help a little bit:)

Best wishes
Radek Kaminski
1) Warsaw University of Technology, Department of Ch= emistry
2) Warsaw University, Department of Chemistry, Division of Cryst= allography

2008/8/7 Hemant Srivastava hemantkrsri%gmail.com <owner-chemistry]|[ccl.net>

Sent to CCL by: "Hemant Srivastava" [hemantkrsri+*+gmail.com]
Dear Shabbir,

For fixing diahedral angle you can write following in input file al last. D 1 2 3 4 F
where 1 2 3 4 are atom numbers.

For the other problem you have I think you should try different
method/basis or solvent calculation.

Hope it will help.

Hemant Kumar Srivastava,
The Hebrew University of Jerusalem
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D


On 8/6/08, Mr shabbir shabbir*_*nenu.edu.cn <owner-chemistry\a/ccl.net> wrote:
>
>  Sent to CCL by: "Mr  shabbir" [shabbir__nenu.edu.cn]
>  Hello CCL users!
>  I am a in some confusion want to explain it. Please If some one = have an idea let me know also.
>  I have taken a crystallographic structure and optimized it using= Gaussian03 with C2 symmetry and b3lyp/6-31G* method. After optimization it= gave me a round about planer structure. After this I have calculated its U= V and IR spectra that is in good agreement with experimental values but the= crystallographic structure has a dihedral angle 40 degree with side pyrrol= rings which is not in my optimized structure. So can I say that my Gasspha= se optimized structure is reliable on the basis of calculated experimental = values and start my futher calculations? Secondly I tried to freeze that di= hedral angle using guessview but it could not freeze during optimization. H= ow to freeze dihedral angle during optimization so that it will not change = during calculations?
>   Mr.Shabbir
>  Northeast normal university Changchun
>  P.R.China
>  shabbir++nenu.e= du.cn>
>
>



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------=_Part_43288_28815050.1218203842967-- From owner-chemistry@ccl.net Fri Aug 8 16:21:00 2008 From: "Nancy Ann Neale nealen!A!mail.nih.gov" To: CCL Subject: CCL: SAR predictions for this paticular question Message-Id: <-37523-080808161218-20135-sNJ1RYg7iYXabE68OhbORg++server.ccl.net> X-Original-From: "Nancy Ann Neale" Date: Fri, 8 Aug 2008 16:12:14 -0400 Sent to CCL by: "Nancy Ann Neale" [nealen#,#mail.nih.gov] I am looking for recommendations for SAR softawre for a specific problem. What we have at this point is approximately 50 compounds that have bee qualitately analyzed for activity in a certain cell. We haven't structural data on the surface protein that shuttles substrates accross the membrane, but that is only the first step in detrmining what a good canddiate is. We have 'downstream' data on these compounds with respect to activity, IC50, and a selectivity ratio. My first thought is AutoDock, but am concerned that may not do the trick because of our lack of structural data of that protein. My goal is to train some program with the good amount of data we have to recognize adn ultimately predict reasonable candidates in the future for this application. Any suggestions are most welcome. Best regards, Nancy From owner-chemistry@ccl.net Fri Aug 8 17:38:01 2008 From: "Hamdy Saad El Sheshtawy h.elsheshtawy~~jacobs-university.de" To: CCL Subject: CCL: thermodynamic calculations Message-Id: <-37524-080808101843-15559-iVy4L0k3XofCT/NNBFGWSQ%server.ccl.net> X-Original-From: "Hamdy Saad El Sheshtawy" Date: Fri, 8 Aug 2008 10:18:39 -0400 Sent to CCL by: "Hamdy Saad El Sheshtawy" [h.elsheshtawy ~ jacobs-university.de] Dear all, I am doing some calculations on the transition state optemizations and I want to calculate the entropy from the thermodynamics outputs. can any one tell me how to calculate the entropy the enthalby and the free energy. best Hamdy From owner-chemistry@ccl.net Fri Aug 8 18:13:01 2008 From: "Alvaro Vazquez-Mayagoitia vama- -xanum.uam.mx" To: CCL Subject: CCL: software for monitor a coordinate (angle) in a XYZ movie Message-Id: <-37525-080808150159-1400-EtOfFtEPOf9Aegy1B/lwfw++server.ccl.net> X-Original-From: "Alvaro Vazquez-Mayagoitia" Date: Fri, 8 Aug 2008 15:01:55 -0400 Sent to CCL by: "Alvaro Vazquez-Mayagoitia" [vama]~[xanum.uam.mx] Dear CCL-forum readers, I' like to follow an especific coordinate (an angle) in a XYZ movie. Do you know a software with this capability? Ive found useful MOLDEN but just for monitor distances. Many thanks in advance. Alvaro From owner-chemistry@ccl.net Fri Aug 8 22:45:00 2008 From: "Lorena Romero lorena.webmaster---gmail.com" To: CCL Subject: CCL:G: thermodynamic calculations Message-Id: <-37526-080808224145-31140-SeJ9tFt3NUkDlIwi70iy1Q|*|server.ccl.net> X-Original-From: "Lorena Romero" Content-Type: multipart/alternative; boundary="----=_Part_59894_30768967.1218245959666" Date: Fri, 8 Aug 2008 21:39:19 -0400 MIME-Version: 1.0 Sent to CCL by: "Lorena Romero" [lorena.webmaster:+:gmail.com] ------=_Part_59894_30768967.1218245959666 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline You can read the file "Thermo" in Gaussian webpage as an introduction, and then looking at szabo=B4s reference book cited there. But, being more specific DG =3D DH - TDS ; DS =3D (DH - DG) / T Where DX =3D Xtransition state - Xreactant. T =3D temperature (Kelvin) You got the enthalpy and the free energy from the output file. Be careful with the units, (hartrees). 2008/8/8 Hamdy Saad El Sheshtawy h.elsheshtawy~~jacobs-university.de < owner-chemistry]|[ccl.net> > > Sent to CCL by: "Hamdy Saad El Sheshtawy" [h.elsheshtawy ~ > jacobs-university.de] > Dear all, > I am doing some calculations on the transition state optemizations and I > want to calculate the entropy from the thermodynamics outputs. can any on= e > tell me how to calculate the entropy the enthalby and the free energy. > best > Hamdy > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 "La alegr=EDa est=E1 en la lucha, en el esfuerzo, en el sufrimiento que sup= one la lucha y no en la victoria." Mahatma Gandhi ------=_Part_59894_30768967.1218245959666 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
You can read the file "Thermo" in Gaussian webpa= ge as an introduction, and then looking at szabo=B4s reference book cited t= here.

But, being more specific DG =3D DH - TDS ; DS =3D = (DH - DG) / T

Where DX =3D Xtransition state - Xreactant.
<= br>
T =3D temperature (Kelvin)

You got the= enthalpy and the free energy from the output file.

Be careful with the units, (hartrees).


<= div>
2008/8/8 Hamdy Saad El Sheshtawy h.elsheshta= wy~~jacobs-university.de <owner-chemistry]|[= ccl.net>

Sent to CCL by: "Hamdy Saad El Sheshtawy" [h.elsheshtawy ~ jacobs-university.de]
Dear all,
I am doing some calculations on the transition state optemizations and I wa= nt to calculate the entropy from the thermodynamics outputs. can any one te= ll me how to calculate the entropy the enthalby and the free energy.
best
Hamdy



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--
"La alegr=EDa est= =E1 en la lucha, en el esfuerzo, en el sufrimiento que supone la lucha y no= en la victoria."=09
Mahatma Gandhi
------=_Part_59894_30768967.1218245959666--