From owner-chemistry@ccl.net Wed Aug 25 03:31:00 2010 From: "Vincent Leroux vincent.leroux#,#loria.fr" To: CCL Subject: CCL: Literature of current status and perspective of comp. chemistry Message-Id: <-42612-100825024316-17115-eehSQPooS8qklMXfOjaEPg*server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 25 Aug 2010 08:43:07 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux-#-loria.fr] Hi, Some good recent papers: O'Donoghue SI, Goodsell DS, Frangakis AS, et al. Visualization of macromolecular structures. Nature Meth. 2010;7(3):S42-S55. Cooper S, Khatib F, Treuille A, et al. Predicting protein structures with a multiplayer online game. Nature. 2010;466(7307):756-760. Stone JE, Hardy DJ, Ufimtsev IS, Schulten K. GPU-accelerated molecular modeling coming of age. J Mol Graph Model. 2010 in the press. For more, Pubmed and Google Scholar are your friends Regards, VL Le 24/08/10 21:30, William Wei william.lh.wei,+,gmail.com a écrit : > Sent to CCL by: "William Wei" [william.lh.wei**gmail.com] > Dear All, > > I am looking for some literature on the current status and perspective of computational chemistry. Could anybody suggest some papers? > > Thank you very much, > William> > > From owner-chemistry@ccl.net Wed Aug 25 08:20:00 2010 From: "Sandhya Rai sandhyachemistry30_._gmail.com" To: CCL Subject: CCL:G: regarding basis set Message-Id: <-42613-100825002710-25285-8uvwtQyoolytcVgiM9JNvQ[a]server.ccl.net> X-Original-From: Sandhya Rai Content-Type: multipart/alternative; boundary=0016e647586612d9c1048e9e4b42 Date: Wed, 25 Aug 2010 13:27:02 +0900 MIME-Version: 1.0 Sent to CCL by: Sandhya Rai [sandhyachemistry30{=}gmail.com] --0016e647586612d9c1048e9e4b42 Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: quoted-printable Thankyou so much. This site is really very helpfull. Thanks a lot, sir. 2010/8/25 Jamin Krinsky jamink-x-berkeley.edu > > Sent to CCL by: Jamin Krinsky [jamink/a\berkeley.edu] > Hi Sandhya, > > There is a tutorial for custom basis set input in Gaussian on our > website: http://glab.cchem.berkeley.edu/glab/faqs/gauss_custombasis.html. > There are several correct methods but I think you will need Example > #4. Hope this helps. > > Regards, > Jamin > > > 2010/8/24 Sandhya Rai sandhyachemistry30---gmail.com ccl.net>: > > Dear sir, > > Thanks for your consideration towards my problem. > > Sir the basis functions I have refered to use the Troullier- > > Martins pseudopotentials. I have all the parameters available > > but do not know how to give the input for the basis set using > > gen keyword. I have tried many times but it is not reading the > > given basis parameters even though I have written '0'. Please > > suggest me any clue to this. I be highly obliged. > > Thanks in advance! > > > > On Tue, Aug 24, 2010 at 10:31 AM, tapang(0)barc.gov.in > > wrote: > >> > >> Sent to CCL by: tapang!A!barc.gov.in > >> Hello Sandhya, > >> Does the term "TMDZ" indicate "Transition Metal Double Zeta " Basis? > >> Please check. > >> Although I don't use Gaussian, however, I have not come accross any > basis > >> set name either with TMDZ or TMSZ. > >> Regards, > >> Tapan Ghanty > >> _____________________________________ > >> Dr. Tapan K Ghanty > >> Theoretical Chemistry Section > >> Chemistry Group, Mod. Labs. > >> Bhabha Atomic Research Centre > >> Trombay, Mumbai 400085, INDIA > >> Tel: +91-22-2559-5089 (O) > >> +91-22-2550-3763 (R) > >> Fax: +91-22-25505151 > >> Email: tapang[-]barc.gov.in > >> _____________________________________ > >> > >> > I don't think such basis sets are available in Gaussian 03 package. > The > >> > only way is to input the ECP basis set by your hand with keyword > "gen". > >> > Since there is no TMDZ and TMSZ basis set in EMSL webpage, I think y= ou > >> > should look for the papers and generate the input file by yourself. > >> > I have found a paper providing the Troullier-Martins pseudopotential > for > >> > silver and gold. I hope such kind of potential is the potential TMDZ > and > >> > TMSZ ECP basis sets use. Google it if you are interested in it or > email > >> > me. I think there is also such papers for other elements. Try to fin= d > >> > these papers and make your input file with these parameters. > >> > > >> > > >> > Best regards, > >> > > >> > 2010-08-23 > >> > > >> > > >> > > >> > fmying > >> > > >> > > >> > > >> > =B7=A2=BC=FE=C8=CB: "Sandhya Rai sandhyachemistry30++gmail.com" > >> > > >> > =B7=A2=CB=CD=CA=B1=BC=E4: 2010-08-23 21:28 > >> > =D6=F7 =CC=E2: CCL:G: regarding basis set > >> > =CA=D5=BC=FE=C8=CB: "Ying, Fuming " > >> > > >> > > >> > > >> > > >> > Dear All, > >> > I'm a graduate student. I want to use the ECP TMDZ and TMSZ basis s= et > >> > for > >> > my calculations. I have read a couple of papers which have made use = of > >> > this set in Gaussian 03 package but I don't find the option for this > in > >> > gaussian > >> > Actually, I'm doing studies on gold nanoparticles & wished to use th= is > >> > basis set. But, I find no clue to use this. > >> > Kindly suggest me the right keyword, or suggest me how to proceed. > >> > Thanks in advance. > >> > Regards > >> > -- > >> > Sandhya Rai > >> > Persuing Ph.D > >> > Centre of Computational Natural Sciences & Bioinformatics > >> > International Institute of Information & Technology > >> > Gachibowli, Hyderabad.>> E-mail to subscribers: CHEMISTRY]^[ccl.neto= r use:>> > >> E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.net or use>> > >> > > > > > > > > -- > > Sandhya Rai > > Persuing Ph.D > > Centre of Computational Natural Sciences & Bioinformatics > > International Institute of Information & Technology > > Gachibowli, Hyderabad. > > > > > > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink/a\berkeley.edu, 510-643-0616 > http://glab.cchem.berkeley.edu > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Sandhya Rai Persuing Ph.D Centre of Computational Natural Sciences & Bioinformatics International Institute of Information & Technology Gachibowli, Hyderabad. --0016e647586612d9c1048e9e4b42 Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: quoted-printable Thankyou so much.
This site is really very helpfull.
 Thanks a l= ot, sir.

2010/8/25 Jamin Krinsky jamink-x-berkeley.edu <owner-chemistry..ccl.net>

Sent to CCL by: Jamin Krinsky [jamink/a\berkeley.edu]
Hi Sandhya,

There is a tutorial for custom basis set input in Gaussian on our
website: http://glab.cchem.berkeley.edu/glab/faqs/gauss_= custombasis.html.
There are several correct methods but I think you will need Example
#4. Hope this helps.

Regards,
Jamin


2010/8/24 Sandhya Rai sandhyachemistry30---gmail.com <owner-chemistry/a\ccl.net>:
> Dear sir,
> Thanks for your consideration towards my problem.
> Sir the basis functions I have refered to use the Troullier-
> Martins pseudopotentials. I have all the parameters available
> but do not know how to give the input for the basis set using
>  gen keyword. I have tried many times but it is not reading the >  given basis parameters even though I have written '0'. P= lease
>  suggest me any clue to this. I be highly obliged.
> Thanks in advance!
>
> On Tue, Aug 24, 2010 at 10:31 AM, tapang(0)barc.gov.in
> <owner-chemistry]^[ccl= .net> wrote:
>>
>> Sent to CCL by: tapang!A!barc.gov.in
>> Hello Sandhya,
>> Does the term  "TMDZ" indicate "Transition Met= al Double Zeta " Basis?
>> Please check.
>> Although I don't use Gaussian, however, I have not come accros= s any basis
>> set name either with TMDZ or TMSZ.
>> Regards,
>> Tapan Ghanty
>> _____________________________________
>> Dr. Tapan K Ghanty
>> Theoretical Chemistry Section
>> Chemistry Group, Mod. Labs.
>> Bhabha Atomic Research Centre
>> Trombay, Mumbai 400085, INDIA
>> Tel: +91-22-2559-5089 (O)
>>     +91-22-2550-3763 (R)
>> Fax: +91-22-25505151
>> Email: tapang[-]b= arc.gov.in
>> _____________________________________
>>
>> > I don't think such basis sets are available in Gaussian 0= 3 package. The
>> > only way is to input the ECP basis set by your hand with keyw= ord "gen".
>> > Since there is no TMDZ and TMSZ basis set in EMSL webpage, I = think you
>> > should look for the papers and generate the input file by you= rself.
>> > I have found a paper providing the Troullier-Martins pseudopo= tential for
>> > silver and gold. I hope such kind of potential is the potenti= al TMDZ and
>> > TMSZ ECP basis sets use. Google it if you are interested in i= t or email
>> > me. I think there is also such papers for other elements. Try= to find
>> > these papers and make your input file with these parameters.<= br> >> >
>> >
>> > Best regards,
>> >
>> > 2010-08-23
>> >
>> >
>> >
>> > fmying
>> >
>> >
>> >
>> > =B7=A2=BC=FE=C8=CB: "Sandhya Rai sandhyachemistry30++gmail.com"
>> > <owner-chemistry[-]ccl.net>
>> > =B7=A2=CB=CD=CA=B1=BC=E4: 2010-08-23 21:28
>> > =D6=F7 =CC=E2: CCL:G: regarding basis set
>> > =CA=D5=BC=FE=C8=CB: "Ying, Fuming " <fmying[-]gmail.com>
>> >
>> >
>> >
>> >
>> > Dear All,
>> >  I'm a graduate student. I want to use the ECP TMDZ = and TMSZ basis set
>> > for
>> > my calculations. I have read a couple of papers which have ma= de use of
>> > this set in Gaussian 03 package but I don't find the opti= on for this in
>> > gaussian
>> > Actually, I'm doing studies on gold nanoparticles & w= ished to use this
>> > basis set. But, I find no clue to use this.
>> > Kindly suggest me the right keyword, or suggest me how to pro= ceed.
>> > Thanks in advance.
>> > Regards
>> > --
>> > Sandhya Rai
>> > Persuing Ph.D
>> > Centre of Computational Natural Sciences & Bioinformatics=
>> > International Institute of Information & Technology
>> > Gachibowli, Hyderabad.>> E-mail to subscrib= ers: CHEMISTRY]^[ccl.net o= r use:>>
>> E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.net or use>>
>>
>
>
>
> --
> Sandhya Rai
> Persuing Ph.D
> Centre of Computational Natural Sciences & Bioinformatics
> International Institute of Information & Technology
> Gachibowli, Hyderabad.
>
>



--
Jamin L Krinsky, Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall, University of California, Berkeley, CA 94720
jamink/a\berkeley.edu= , 510-643-0616
http://glab.cc= hem.berkeley.edu



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--
Sandhya Rai=
Persuing Ph.D
Centre of Computational Natural Sciences & Bioinfo= rmatics
International Institute of Information & Technology
Gachi= bowli, Hyderabad.

--0016e647586612d9c1048e9e4b42-- From owner-chemistry@ccl.net Wed Aug 25 19:11:00 2010 From: "W Flak williamflak_._yahoo.com" To: CCL Subject: CCL: Drawing Software Message-Id: <-42614-100825190818-7506-NH0LBnK5uxEEXkmyJeBTqg^server.ccl.net> X-Original-From: "W Flak" Date: Wed, 25 Aug 2010 19:08:16 -0400 Sent to CCL by: "W Flak" [williamflak{=}yahoo.com] Dear CCL I was wondering if there is a free software to draw the reaction mechanism, energy levels of reactants, transition state and products, where I use chemdraw but the graph is not organised well. Thanks in advance Flak From owner-chemistry@ccl.net Wed Aug 25 21:09:00 2010 From: "Venable, Richard (NIH/NHLBI) E venabler-.-nhlbi.nih.gov" To: CCL Subject: CCL: Drawing Software Message-Id: <-42615-100825210625-6165-VYyAPpYh18JHVmoLl/4ALA\a/server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 25 Aug 2010 21:05:36 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler]![nhlbi.nih.gov] On Linux (Ubuntu), I've found the combination of chemtool and the venerable xfig program works fairly well. Draw the individual molecules with chemtool, save each to a file, then export the drawing in encapsulated postscript format. For markup, the xfig program can read, place, and display .eps files as objects, and allows the addition of annotation as text, lines, arrows, etc. to create a final complex figure. You could also add structures to an energy vs. reaction coordinate plot this way, assuming the plotting program can produce postscript output. The ps2epsi command (part of ghostscript) can be used to encapsulate .ps to .eps, for programs that don't offer .eps output. Regards, -- 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 8/25/10 7:08 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: Sent to CCL by: "W Flak" [williamflak{=}yahoo.com] Dear CCL I was wondering if there is a free software to draw the reaction mechanism, energy levels of reactants, transition state and products, where I use chemdraw but the graph is not organised well. Thanks in advance Flak