From owner-chemistry@ccl.net Fri Aug 19 00:38:00 2011 From: "Rajagopala Reddy Seelam rajagopalaseelam[A]gmail.com" To: CCL Subject: CCL: Stuttgart pseudopotentials Message-Id: <-45290-110818234913-11845-Us7R0CXd3lpQLrU1UgPG8Q(~)server.ccl.net> X-Original-From: "Rajagopala Reddy Seelam" Date: Thu, 18 Aug 2011 23:49:06 -0400 Sent to CCL by: "Rajagopala Reddy Seelam" [rajagopalaseelam|gmail.com] Hi Carlos, I think the following web page will do it for you. http://glab.cchem.berkeley.edu/glab/faqs/gauss_custombasis.html use the format to use pseudo potentials and get the potentials from Stuttgart webpage. regards S.Rajagopala Reddy Prof.Mahapatra lab School of Chemistry University of Hyderabad From owner-chemistry@ccl.net Fri Aug 19 04:21:00 2011 From: "Andrew v Voronkov drugdesign+*+yandex.ru" To: CCL Subject: CCL: free protein viewer/editor where it is possible to depict Connolly sur Message-Id: <-45291-110818111732-9531-d/wH0Lt4Jgjp6vwyQeVkaw^-^server.ccl.net> X-Original-From: "Andrew v Voronkov" Date: Thu, 18 Aug 2011 11:17:28 -0400 Sent to CCL by: "Andrew v Voronkov" [drugdesign-$-yandex.ru] Dear CCL users, can you please recommend some free protein viewer/editor where it is possible to depict Connolly surface of the protein colored by hydrophobicity? Sincerely yours, Andrew From owner-chemistry@ccl.net Fri Aug 19 05:11:00 2011 From: "Sergio Manzetti sergio.manzetti[*]gmail.com" To: CCL Subject: CCL: Illustrating Frequencies as a function of Color Message-Id: <-45292-110819050951-7878-/kQqxWRPtXBwAsOfnTCXPg^^server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=20cf307d04c6010f5904aad8171d Date: Fri, 19 Aug 2011 11:09:42 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti*_*gmail.com] --20cf307d04c6010f5904aad8171d Content-Type: text/plain; charset=ISO-8859-1 Dear users, does anyone know how one can illustrate the numerous vibrational frequencies of a molecule through a color-illustration? For instance, the higher the frequency, the more red the color, and the lower the more blue. Thanks Sergio --20cf307d04c6010f5904aad8171d Content-Type: text/html; charset=ISO-8859-1 Dear users, does anyone know how one can illustrate the numerous vibrational frequencies of a molecule through a color-illustration?

For instance, the higher the frequency, the more red the color, and the lower the more blue.

Thanks

Sergio
--20cf307d04c6010f5904aad8171d-- From owner-chemistry@ccl.net Fri Aug 19 07:15:00 2011 From: "Sanjay Bharathwaj computationalchemist * gmail.com" To: CCL Subject: CCL: Simulation of Electron Diffraction Message-Id: <-45293-110819070253-29184-z5416we8AKZrGd2PVZhJXA(a)server.ccl.net> X-Original-From: Sanjay Bharathwaj Content-Type: multipart/alternative; boundary=20cf303a2dc55ee5c004aad9ab99 Date: Fri, 19 Aug 2011 13:02:46 +0200 MIME-Version: 1.0 Sent to CCL by: Sanjay Bharathwaj [computationalchemist * gmail.com] --20cf303a2dc55ee5c004aad9ab99 Content-Type: text/plain; charset=ISO-8859-1 Dear Friends, I have couple of crystal structures in .cif format and I wanted to simulate the electron diffraction data. Hence, could you please let me know if there are any freeware available to do this job. I will be glad to have answers and i thank you all in advance. My best regards, SB -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, India. --20cf303a2dc55ee5c004aad9ab99 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Friends,
<= br>
I have couple of crystal structures in .cif format and
I = wanted to simulate the electron diffraction data.

Hence, could you please let me know if there are any fr= eeware available
to do this job.

I will = be glad to have answers and i thank you all in advance.

My best regards,
SB

--
= Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra Institute of Technol= ogy,
India.
--20cf303a2dc55ee5c004aad9ab99-- From owner-chemistry@ccl.net Fri Aug 19 09:30:01 2011 From: "Gerald Knizia knizia]*[theochem.uni-stuttgart.de" To: CCL Subject: CCL: What is wrong with M06 vibrational frequencies Message-Id: <-45294-110819075515-17820-h3+8LACW4f12LiGw3m5arA!A!server.ccl.net> X-Original-From: Gerald Knizia Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 19 Aug 2011 07:55:06 -0400 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia\a/theochem.uni-stuttgart.de] Adel El-Azhary azhary---ksu.edu.sa wrote: > I am not sure that anyone of you experienced this problem before or knows a solution for it. I am calculating vibrational frequencies at the HF, B3LYP, M06, M06L, M062x, M06HF and MP2 levels of a molecule. All vibrational frequencies are real at the HF, B3LYP and MP2 levels but at the M06, M06L, M062x and M06HF levels, one or more vibrational frequency is imaginary. The M06 (and the other M* functionals) are basically fitted to death[1] on a large training set in order to give good thermochemistry values. They are not fitted on potential energy surfaces. While in general this apparently works well, you have to be wary. It's only to be expected that they break for some molecules and applications which are sufficiently different from what they are fitted for[2]. If you are sure that your geometries with the different methods converged to equivalent structures, you maybe shouldn't worry about that too much and simply use some other theoretical method. [1] They have over 30 fitting parameters, additionally to the choice of the functional form. [2] ...or which in general cannot be reliably represented by DFT methods, like dispersive interactions or strong correlations. Maybe HF and B3LYP anr just as wrong, but in a different way, which causes them to erroneously report positive PES curvature. To be absolutely sure about that you would need to repeat your calculation with a more accurate wave function method, but this might be unaffordable. -- Gerald Knizia From owner-chemistry@ccl.net Fri Aug 19 11:09:00 2011 From: "Tijesunimi Odebode tijesunimi[]yahoo.com" To: CCL Subject: CCL:G: CHARMM Message-Id: <-45295-110818120154-28504-MpVT5GWsqZ1k0NgZCcSLdQ .. server.ccl.net> X-Original-From: "Tijesunimi Odebode" Date: Thu, 18 Aug 2011 12:01:51 -0400 Sent to CCL by: "Tijesunimi Odebode" [tijesunimi*o*yahoo.com] Hello All, I am new to CHARMM so I have a very basic question to ask, and I will be grateful if someone could help me out. I just finished energy optimization of my ligand using gaussian so I have the xyz coordinates. I am about to do some CHARMM work on that same ligand so I have completed my topology file, except for the IC table. Can someone explain to me how to generate an IC table from the xyz coordinates using the IC generate command or if there is any other way to do it. I am aware that I probably need to create a .inp file that will serve as my run script but I don't know how to go about it. Is there a site I can go that has a template I can follow to do this? Thanks a lot for your help. From owner-chemistry@ccl.net Fri Aug 19 12:58:00 2011 From: "Carlos T Nieto eneas*_*usal.es" To: CCL Subject: CCL:G: Bromine basis sets in Jaguar Message-Id: <-45296-110819092337-32617-dy/YMzUo1WZFWld2orMTWA(0)server.ccl.net> X-Original-From: "Carlos T Nieto" Date: Fri, 19 Aug 2011 09:23:33 -0400 Sent to CCL by: "Carlos T Nieto" [eneas{=}usal.es] I've begun some theoretical reaction studies, bromine additions to olefines, and apparently, 6-31G as a basis sets is not available in Jaguar (only to Ar or Zn). The curious fact is Gaussian includes the complete 3rd row to this basis. Searching literature i've found that Jaguar doesnt include the lastest basis set enlargement (DOI: 10.1002/jcc.1058). The question is what basis set and theory do you recommend me for this bromine type reactions. There are bromine type additions to olefins, in which a bromonium type intermidiate is one of the structures to optimize. Thanks a lot. From owner-chemistry@ccl.net Fri Aug 19 13:33:01 2011 From: "Steve Williams willsd(_)appstate.edu" To: CCL Subject: CCL:G: What is wrong with M06 vibrational frequencies Message-Id: <-45297-110819103147-24279-HszkON+GZhAiC4DVQgaY2A:_:server.ccl.net> X-Original-From: Steve Williams Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 19 Aug 2011 10:31:25 -0400 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd() appstate.edu] On 08/19/2011 07:55 AM, Gerald Knizia knizia]*[theochem.uni-stuttgart.de wrote: > > Sent to CCL by: Gerald Knizia [knizia\a/theochem.uni-stuttgart.de] > Adel El-Azhary azhary---ksu.edu.sa wrote: >> I am not sure that anyone of you experienced this problem before or >> knows a solution for it. I am calculating vibrational frequencies at >> the HF, B3LYP, M06, M06L, M062x, M06HF and MP2 levels of a molecule. >> All vibrational frequencies are real at the HF, B3LYP and MP2 levels >> but at the M06, M06L, M062x and M06HF levels, one or more vibrational >> frequency is imaginary. > > The M06 (and the other M* functionals) are basically fitted to > death[1] on a large training set in order to give good thermochemistry > values. They are not fitted on potential energy surfaces. While in > general this apparently works well, you have to be wary. It's only to > be expected that they break for some molecules and applications which > are sufficiently different from what they are fitted for[2]. If you > are sure that your geometries with the different methods converged to > equivalent structures, you maybe shouldn't worry about that too much > and simply use some other theoretical method. > > [1] They have over 30 fitting parameters, additionally to the choice > of the functional form. > [2] ...or which in general cannot be reliably represented by DFT > methods, like dispersive interactions or strong correlations. Maybe HF > and B3LYP anr just as wrong, but in a different way, which causes them > to erroneously report positive PES curvature. To be absolutely sure > about that you would need to repeat your calculation with a more > accurate wave function method, but this might be unaffordable. This is a good point. If these M* functionals are "broken" for anything but thermochemistry at single points, you might be able to have gradients and second derivatives "broken" in the same way. I think you are using gaussian for these calculations, so (if you can afford it), you might want to try opt=(calcall,tight) with your ultrafine grid. This will use the M* analytic Hessian to guide the optimization at every step. This is guaranteed to be really slow, but will take fewer steps in the optimization. There is no need for a subsequent freq calculation since this automatically reported on the converged geometry. Steve Williams From owner-chemistry@ccl.net Fri Aug 19 14:08:01 2011 From: "Elaine Meng meng-*-cgl.ucsf.edu" To: CCL Subject: CCL: Simulation of Electron Diffraction Message-Id: <-45298-110819124931-28726-FL6ms6n2RLY2/aHYctg5Ug||server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 19 Aug 2011 12:49:26 -0400 Sent to CCL by: "Elaine Meng" [meng_+_cgl.ucsf.edu] Hi Sanjay, In Chimera, the "molmap" command can be used to simulate a density map from atomic coordinates. http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html Chimera is free for noncommercial use. http://plato.cgl.ucsf.edu/chimera/download.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Fri Aug 19 14:42:00 2011 From: "Elaine Meng meng a cgl.ucsf.edu" To: CCL Subject: CCL: Connolly surface with hydrophobicity coloring Message-Id: <-45299-110819125107-4100-XZRDMublr/wV0SdRz5ONvw(!)server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 19 Aug 2011 12:51:03 -0400 Sent to CCL by: "Elaine Meng" [meng*cgl.ucsf.edu] Hi Andrew, In Chimera you can show the Connolly molecular surface colored by amino acid hydrophobicity -- it uses a lookup table of amino acid hydrophobicity values, however, and does not calculate a distance-dependent "potential". Hydrophobicity coloring is easily done by simply choosing the "hydrophobicity surface" option from the Presets menu, or with more steps you can customize the coloring. This tutorial includes an example: http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html Chimera is free for noncommercial use. http://plato.cgl.ucsf.edu/chimera/download.html For hydrophobicity "potential" calculations, you may want to take a look at the Platinum web server: http://model.nmr.ru/platinum/ I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Fri Aug 19 15:18:00 2011 From: "Wendy Warr wendy:-:warr.com" To: CCL Subject: CCL: Report on Spring 2011 ACS National Meeting Message-Id: <-45300-110819125543-16564-t2MwsYC8ko5hrjZCXV6JCQ]_[server.ccl.net> X-Original-From: "Wendy Warr" Date: Fri, 19 Aug 2011 12:55:38 -0400 Sent to CCL by: "Wendy Warr" [wendy _ warr.com] Chemical Information and Computation 2011, Number One 241st ACS National Meeting and Exposition: Anaheim, CA, March 27-31, 2011 Our 37th ACS report has transcripts of papers from symposia on: reaction classification and synthesis planning the Internet and chemistry open data, open science, open knowledge challenges in industrial computational methods plus six months' worth of news from about 75 companies. Contents list and order forms at http://www.warr.com. Note that the report itself will not be on the Web. Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./Fax +44 (0)1477 533837 wendy::warr.com http://www.warr.com From owner-chemistry@ccl.net Fri Aug 19 15:53:01 2011 From: "Venable, Richard (NIH/NHLBI) E venabler%%nhlbi.nih.gov" To: CCL Subject: CCL:G: CHARMM Message-Id: <-45301-110819132352-12210-XEGze+UI5r58Ul8PhtoYgA*|*server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 19 Aug 2011 13:23:43 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler_._nhlbi.nih.gov] The forums at www.charmm.org may be useful as you proceed with CHARMM. If you have Cartesian coordinates, the IC entries may not not be needed at all; they are mostly used for model building in the absence of Cartesian coordinates. The IC GENERATE command is not suitable for making an IC table for the topology file, esp. for rings. The best IC tables are hand edited; only the dihedral angles need to to be specified, and only for the heavy atoms; HBUILD places H atoms w/o needing IC entries. The IC PARAM command will fill in bond lengths and angles > from the parameters. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 8/18/11 12:01 PM, "Tijesunimi Odebode tijesunimi[]yahoo.com" wrote: > >Sent to CCL by: "Tijesunimi Odebode" [tijesunimi*o*yahoo.com] >Hello All, > >I am new to CHARMM so I have a very basic question to ask, and I will be >grateful if someone could >help me out. I just finished energy optimization of my ligand using >gaussian so I have the xyz >coordinates. I am about to do some CHARMM work on that same ligand so I >have completed my >topology file, except for the IC table. Can someone explain to me how to >generate an IC table from the >xyz coordinates using the IC generate command or if there is any other >way to do it. I am aware that I >probably need to create a .inp file that will serve as my run script but >I don't know how to go about it. >Is there a site I can go that has a template I can follow to do this? >Thanks a lot for your help. From owner-chemistry@ccl.net Fri Aug 19 16:28:01 2011 From: "Shobana Sundaram/FS/VCU ssundaram!=!vcu.edu" To: CCL Subject: CCL:G: CHARMM Message-Id: <-45302-110819141405-30600-mRUrwddZPKD1zs/G7shebA]~[server.ccl.net> X-Original-From: Shobana Sundaram/FS/VCU Content-Type: multipart/alternative; boundary="=_alternative 00641C98852578F1_=" Date: Fri, 19 Aug 2011 14:13:46 -0400 MIME-Version: 1.0 Sent to CCL by: Shobana Sundaram/FS/VCU [ssundaram*o*vcu.edu] This is a multipart message in MIME format. --=_alternative 00641C98852578F1_= Content-Type: text/plain; charset="US-ASCII" Hi Tijesunimi Odebode, Yes, the same question exists in charmm forum answered by Dr. Nilsson. See this link http://www.charmm.org/ubbthreads-7-5-3/ubbthreads.php?ubb=showflat&Number=23043 > From this link, you can get to most of what one needs from charmm http://www.charmmtutorial.org/index.php/CHARMM_Tutorial Good Luck! -shobana > From: "Tijesunimi Odebode tijesunimi[]yahoo.com" To: "Sundaram, Shobana " Date: 08/19/2011 11:51 AM Subject: CCL:G: CHARMM Sent by: owner-chemistry+ssundaram==vcu.edu-,-ccl.net Sent to CCL by: "Tijesunimi Odebode" [tijesunimi*o*yahoo.com] Hello All, I am new to CHARMM so I have a very basic question to ask, and I will be grateful if someone could help me out. I just finished energy optimization of my ligand using gaussian so I have the xyz coordinates. I am about to do some CHARMM work on that same ligand so I have completed my topology file, except for the IC table. Can someone explain to me how to generate an IC table from the xyz coordinates using the IC generate command or if there is any other way to do it. I am aware that I probably need to create a .inp file that will serve as my run script but I don't know how to go about it. Is there a site I can go that has a template I can follow to do this? Thanks a lot for your help.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 00641C98852578F1_= Content-Type: text/html; charset="US-ASCII" Hi Tijesunimi  Odebode,

Yes, the same question exists in charmm forum answered by Dr. Nilsson. See this link
 http://www.charmm.org/ubbthreads-7-5-3/ubbthreads.php?ubb=showflat&Number=23043

From this link, you can get to most of what one needs from charmm

http://www.charmmtutorial.org/index.php/CHARMM_Tutorial


Good Luck!

-shobana









From:        "Tijesunimi Odebode tijesunimi[]yahoo.com" <owner-chemistry-,-ccl.net>
To:        "Sundaram, Shobana " <ssundaram-,-vcu.edu>
Date:        08/19/2011 11:51 AM
Subject:        CCL:G: CHARMM
Sent by:        owner-chemistry+ssundaram==vcu.edu-,-ccl.net




Sent to CCL by: "Tijesunimi  Odebode" [tijesunimi*o*yahoo.com]
Hello All,

I am new to CHARMM so I have a very basic question to ask, and I will be grateful if someone could
help me out. I just finished energy optimization of my ligand using gaussian so I have the xyz
coordinates. I am about to do some CHARMM work on that same ligand so I have completed my
topology file, except for the IC table. Can someone explain to me how to generate an IC table from the
xyz coordinates using the IC generate command or if there is any other way to do it. I am aware that I
probably need to create a .inp file that will serve as my run script but I don't know how to go about it.
Is there a site I can go that has a template I can follow to do this? Thanks a lot for your help.


     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
     http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
     http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
--=_alternative 00641C98852578F1_=--