From owner-chemistry@ccl.net Wed Jun 30 08:07:01 2010 From: "rocky walden rocky.walden19||gmail.com" To: CCL Subject: CCL: Needs your kind help.. Message-Id: <-42220-100630041452-26473-ubKBCpHyTvdU1vpIxYHHBA|a|server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=001636c931e44f6c45048a3af2ba Date: Wed, 30 Jun 2010 13:44:44 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19##gmail.com] --001636c931e44f6c45048a3af2ba Content-Type: text/plain; charset=ISO-8859-1 Hi All, Thank you all for your help in sorting out Turbomole Installation and a question on NMR chemical shielding calculation using Turbomole Tool. Now i have a question for you all.. Few grad students in our group speak about Molecular Dynamic simulations. and i asked them how would you perform an MD simulation of a protein and a docked lignad. ( they just replied me its not the age to know the answer). I am interested in Computational Chemistry and i am yet to finish my Undergraduate course and plnning to take a Masters in Computational Chemistry focusing Drug Discovery. Can any one kindly list the protocols needed for MD simulation.. I wanted to look my protein and ligand changing the conformation after simulation in a water box. what are the basic parameters and suggest me a good book on MD simulations. Regards Walden Matthews R --001636c931e44f6c45048a3af2ba Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All,
=A0Thank you all for your help in sorting out Turbomole Installa= tion and a question on NMR chemical shielding calculation using Turbomole T= ool.
=A0Now i have a question for you all..
=A0Few grad students in o= ur group speak about Molecular Dynamic simulations.
=A0and i asked them how would you perform an MD simulation of a protein and= a docked lignad. ( they just replied me its not the age to know the answer= ).
=A0I am interested in Computational Chemistry and i am yet to finish = my Undergraduate course and plnning to take a Masters in Computational Chem= istry focusing Drug Discovery.
=A0Can any one kindly list the protocols needed for MD simulation..
I wa= nted to look my protein and ligand changing the conformation after simulati= on in a water box.


what are the basic parameters and suggest me = a good book on MD simulations.

Regards
Walden Matthews R
--001636c931e44f6c45048a3af2ba-- From owner-chemistry@ccl.net Wed Jun 30 10:14:00 2010 From: "Sangeetha Subramaniam srdshigella .. gmail.com" To: CCL Subject: CCL: Generating image for small molecules: Message-Id: <-42221-100630101311-9485-MxLSiwNFRbfdn+O/mYfVwA a server.ccl.net> X-Original-From: "Sangeetha Subramaniam" Date: Wed, 30 Jun 2010 10:13:10 -0400 Sent to CCL by: "Sangeetha Subramaniam" [srdshigella . gmail.com] Hi, Can someone suggest me freeware for generating good image files for small molecules. thanks !!! Sangi. From owner-chemistry@ccl.net Wed Jun 30 11:45:00 2010 From: "Esteban Gabriel Vega Hissi egvega(0)gmail.com" To: CCL Subject: CCL: Generating image for small molecules: Message-Id: <-42222-100630114235-14569-tZy5oQnUiPuFIxSF0Biq8A/./server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=0016e6dab034c9f38f048a40d912 Date: Wed, 30 Jun 2010 17:17:03 +0200 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega]*[gmail.com] --0016e6dab034c9f38f048a40d912 Content-Type: text/plain; charset=ISO-8859-1 Yes, VMD and/or PyMol Best Esteban On Wed, Jun 30, 2010 at 4:13 PM, Sangeetha Subramaniam srdshigella .. gmail.com wrote: > > Sent to CCL by: "Sangeetha Subramaniam" [srdshigella . gmail.com] > Hi, > > Can someone suggest me freeware for generating good image files for > small molecules. > > thanks !!! > Sangi.> > > --0016e6dab034c9f38f048a40d912 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Yes,

VMD and/or PyMol

Best

Esteban

On Wed, Jun 30, 2010 at 4:13 PM, Sangeetha Subramaniam srd= shigella .. gmail.com &l= t;owner-chemistry===ccl.net>= ; wrote:

Sent to CCL by: "Sangeetha =A0Subramaniam" [srdshigella . gmail.com]
Hi,

Can someone suggest me freeware for generating good image files for
small molecules.

thanks !!!
Sangi.



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--0016e6dab034c9f38f048a40d912-- From owner-chemistry@ccl.net Wed Jun 30 12:20:01 2010 From: "Deepangi Pandit deepangi.pandit*gmail.com" To: CCL Subject: CCL: Generating image for small molecules: Message-Id: <-42223-100630105538-27051-G9De3jDuegmxgWKl6f1fqQ ~ server.ccl.net> X-Original-From: Deepangi Pandit Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 30 Jun 2010 10:55:22 -0400 MIME-Version: 1.0 Sent to CCL by: Deepangi Pandit [deepangi.pandit::gmail.com] Hi Sangeetha: You can download ISIS Draw for free from the link below but you will have to register. http://www.symyx.com/downloads/ Good luck, Deepa On Wed, Jun 30, 2010 at 10:13 AM, Sangeetha Subramaniam srdshigella .. gmail.com wrote: > > Sent to CCL by: "Sangeetha  Subramaniam" [srdshigella . gmail.com] > Hi, > > Can someone suggest me freeware for generating good image files for > small molecules. > > thanks !!! > Sangi.>      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>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Wed Jun 30 12:54:00 2010 From: "Gert Kiss mail]|[gertkiss.de" To: CCL Subject: CCL: Generating image for small molecules: Message-Id: <-42224-100630120941-16654-8jz0uwivPcI6bYvMDI+YOw,server.ccl.net> X-Original-From: "Gert Kiss" Content-language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 30 Jun 2010 09:09:17 -0700 MIME-Version: 1.0 Sent to CCL by: "Gert Kiss" [mail*|*gertkiss.de] Hi Sangi, You might want to try CYLview (http://www.cylview.org/Home.html). It is free and generates professional images in ready-to-publish quality. Best, Gert -----Original Message----- > From: owner-chemistry+mail==gertkiss.de!A!ccl.net [mailto:owner-chemistry+mail==gertkiss.de!A!ccl.net] On Behalf Of Sangeetha Subramaniam srdshigella .. gmail.com Sent: Wednesday, June 30, 2010 7:13 AM To: Kiss, Gert Subject: CCL: Generating image for small molecules: Sent to CCL by: "Sangeetha Subramaniam" [srdshigella . gmail.com] Hi, Can someone suggest me freeware for generating good image files for small molecules. thanks !!! Sangi.http://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 Wed Jun 30 14:40:00 2010 From: "Aniko Simon aniko^simbiosys.ca" To: CCL Subject: CCL: Generating image for small molecules: Message-Id: <-42225-100630131955-10842-2KYSnAY6tVkvN02Yhy2zYw::server.ccl.net> X-Original-From: "Aniko Simon" Date: Wed, 30 Jun 2010 13:19:54 -0400 Sent to CCL by: "Aniko Simon" [aniko=simbiosys.ca] Hi Sangi, CheVi (Chemical Visualizer) 3D software is a freeware: http://www.simbiosys.com/chevi/index.html exports excellent quality (high resolution) images - good even for huge poster printouts in PNG or EPS file format. Simple to use, and supported for free by a commercial company. To download please fill in a demo request at: http://www.simbiosys.com/products/demo_request.html Best wishes, Aniko -- Aniko Simon, Ph.D. | SimBioSys Inc. | Tel: 1-416-741-4263 http://www.simbiosys.com/ | blog: http://www.simbiosys.com/blog/ Check out the most recent customer quotes about SimBioSys: http://www.simbiosys.com/support/index.html#quotes On June 30, 2010 10:13:10 am Sangeetha Subramaniam srdshigella .. gmail.com wrote: > Sent to CCL by: "Sangeetha Subramaniam" [srdshigella . gmail.com] > Hi, > > Can someone suggest me freeware for generating good image files for > small molecules. > > thanks !!! > Sangi. From owner-chemistry@ccl.net Wed Jun 30 15:15:00 2010 From: "Wolf-D. Ihlenfeldt wdi _ xemistry.com" To: CCL Subject: CCL: AW: Generating image for small molecules: Message-Id: <-42226-100630120117-5131-G0VisV8qzG2MbfhIZ6O2TA!^!server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: de Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 30 Jun 2010 18:01:06 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi/./xemistry.com] If you are talking about 2D images: For academic users, the Cactvs toolkit (www.xemistry.com/academic) is free. This is the software used, for example, to generate the layout and images in the PubChem database. It can write lots of image formats (GIF, PNG, SVG, EPS, WMF, EMF, PDF, PICT, SWF, MIF, all formats on all platforms), with or without generation of 2D coordinates. The generic toolkit will require you to write a short processing script. Xemistry also markets a powerful ready-to-run batch image generator application, but that is commercial software for all users. > -----Ursprüngliche Nachricht----- > Von: owner-chemistry+wdi==xemistry.com^^^ccl.net [mailto:owner- > chemistry+wdi==xemistry.com^^^ccl.net] Im Auftrag von Sangeetha > Subramaniam srdshigella .. gmail.com > Gesendet: Mittwoch, 30. Juni 2010 16:13 > An: Ihlenfeldt, Wolf D > Betreff: CCL: Generating image for small molecules: > > > Sent to CCL by: "Sangeetha Subramaniam" [srdshigella . gmail.com] > Hi, > > Can someone suggest me freeware for generating good image files for > small molecules. > > thanks !!! > Sangi.> To recover the email address of the author of the message, please > change