From owner-chemistry@ccl.net Thu Feb 28 04:06:01 2008 From: "Karin Wichmann wichmann%cosmologic.de" To: CCL Subject: CCL: COSMOtherm / COSMO-RS Training Message-Id: <-36378-080228034942-22637-oL06UMTwNkbLmtknmmkdIA*server.ccl.net> X-Original-From: Karin Wichmann Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 28 Feb 2008 09:19:26 +0100 MIME-Version: 1.0 Sent to CCL by: Karin Wichmann [wichmann/./cosmologic.de] COSMOlogic has a small number of seats available for a free COSMOtherm training on Mar 13. The training is a one-day course covering COSMO-RS theory for fluid thermodynamics and its applications in the areas of chemical engineering and life science. The course will take place at our location in Leverkusen (Germany). For further information please contact us at cosmotherm (AT) cosmologic.de -- ------------------------ Dr. Karin Wichmann COSMOlogic GmbH & Co. KG Burscheider Str. 515 D-51381 Leverkusen Germany Phone +49-2171-73168-3 Fax +49-2171-73168-9 ------------------------ From owner-chemistry@ccl.net Thu Feb 28 06:59:00 2008 From: "soumya s soumya_samineni * rediffmail.com" To: CCL Subject: CCL: visualisation software in linux Message-Id: <-36379-080228065747-18258-AQDUuR9hH5kaAmUZ4I0wOA,+,server.ccl.net> X-Original-From: "soumya s" Date: Thu, 28 Feb 2008 06:57:43 -0500 Sent to CCL by: "soumya s" [soumya_samineni!A!rediffmail.com] Hello It would be nice if some one could suggest a freely available program to build crystals , cut planes and make slabs .. thanx in advance soumya From owner-chemistry@ccl.net Thu Feb 28 09:12:01 2008 From: "mmooney05[#]qub.ac.uk" To: CCL Subject: CCL: AutoDock4 Message-Id: <-36380-080228065128-17555-jez0rMeBnwyGQYpA8sfQhA ~~ server.ccl.net> X-Original-From: mmooney05||qub.ac.uk Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 28 Feb 2008 10:46:12 +0000 Mime-Version: 1.0 Sent to CCL by: mmooney05*qub.ac.uk Hello CCL-ers, Recently I have started to use AutoDock4 on my ubuntu 7.10 PC= =20 and my XP PC. I am currently working on the tutorial, which works fine,=20 until I launch the autodock job. The job runs to =91successful completion= =92=20 when launched from the command line; however I get several warning messages= =20 output as follows: autodock4: WARNING: the atom type (X) of atom number =91y=92 could not be= =20 found; check that this atom type is listed after the =93ligand_types=94 key= word=20 in the DPF, and make sure to add a =93map=94 keyword to the DPF for this at= om=20 type. Note that AutoDock will use the default atom type =3D 1, instead. It should be noted that this warning is output for several atoms. I=20 manually edited the DPF before submitting the AutoDock job so that it=20 contained the atom types that were specified from the warning. I also added= =20 maps to the DPF for each of the missing atom types. I=92m not sure how=20 accurate this is (i.e-when does AutoDock assign atom types) or if there is= =20 a =91better=92 way to fulfil this. Also is there a method to view the atom= =20 types (assigned by autodock) in the GUI/workspace? I would be most grateful for any suggestions/advice regarding this issue. Many Thanx, Maura From owner-chemistry@ccl.net Thu Feb 28 15:49:01 2008 From: "Fedor Goumans fedor.goumans]~[googlemail.com" To: CCL Subject: CCL: visualisation software in linux Message-Id: <-36381-080228113739-17328-xwU1mOd54Oifqkh7XwLX+Q]_[server.ccl.net> X-Original-From: "Fedor Goumans" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 28 Feb 2008 15:40:10 +0000 MIME-Version: 1.0 Sent to CCL by: "Fedor Goumans" [fedor.goumans*o*googlemail.com] Dear Soumya, You might find gdis very helpful: http://sourceforge.net/projects/gdis Which reads and writes many file formats. There's also DLV: http://www.cse.scitech.ac.uk/cmg/DLV/ Helpful if you want to use your structures for CRYSTAL calculations. Hope this helps, Kind regards, Fedor On 28/02/2008, soumya s soumya_samineni * rediffmail.com wrote: > > Sent to CCL by: "soumya s" [soumya_samineni!A!rediffmail.com] > Hello > It would be nice if some one could suggest a freely available program to build crystals , cut planes and make slabs .. > > thanx in advance > soumya> > > From owner-chemistry@ccl.net Thu Feb 28 16:30:01 2008 From: "Diego Vicente Moreno Rodriguez dvmorenor(_)unal.edu.co" To: CCL Subject: CCL: visualisation software in linux Message-Id: <-36382-080228100201-25875-4bm8XK9cdcXkUxY/HZw0zw ~ server.ccl.net> X-Original-From: "Diego Vicente Moreno Rodriguez" Content-Type: multipart/alternative; boundary="----=_Part_1912_3617526.1204207053268" Date: Thu, 28 Feb 2008 08:57:33 -0500 MIME-Version: 1.0 Sent to CCL by: "Diego Vicente Moreno Rodriguez" [dvmorenor=unal.edu.co] ------=_Part_1912_3617526.1204207053268 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Xcrysden is a *crystalline and molecular structure visualisation program*, which aims at display of isosurfaces and contours, which can be superimpose= d on crystalline structures and interactively rotated and manipulated. It can run on most *UNIX* platforms, without any special hardware requirements. http://www.xcrysden.org/ In conjunction with frontend by pwscf is a good tool for building http://www.pwscf.org/ --=20 ---- ___ ___ ___ /\ \ /\ \ /\ \ /::\ \ /::\ \ \:\ \ Diego Moreno /:/\:\__\\:\:\__\ /::\__\ \:\:\/__/ \::/ //:/\/__/ Grupo de Qu=EDmica Te=F3rica \::/ / /:/ / \/__/ Universidad Nacional de Col. \/__/ \/__/ 2008/2/28, soumya s soumya_samineni * rediffmail.com < owner-chemistry.:.ccl.net>: > > > Sent to CCL by: "soumya s" [soumya_samineni!A!rediffmail.com] > Hello > It would be nice if some one could suggest a freely available program to > build crystals , cut planes and make slabs .. > > thanx in advance > soumya > > > > ------=_Part_1912_3617526.1204207053268 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Xcrysden is a crystalline and molecular structure visualisat= ion program, which aims at display of isosurfaces a= nd contours, which can be superimposed on crystalline structures and interactively rotated and manipulate= d. It can run on most UNIX<= /i> platforms, without any special hardware requirements.

http://www.xcrysden.org/

In conjunction = with frontend by pwscf is a good tool for building
http://www.pwscf.org/

--
----         = ;            &n= bsp;    ___     ___  &nbs= p;  ___  
    = ;            &n= bsp;            /\&n= bsp; \   /\  \   /\  \ &n= bsp;
      &= nbsp;           &nbs= p;         /::\  \ /= ::\  \  \:\  \
Diego Moreno  = ;             /= :/\:\__\\:\:\__\ /::\__\
   = ;            &n= bsp;           \:\:\/__/ = \::/  //:/\/__/
Grupo de Qu=EDmica Te= =F3rica    \::/  /  /:/  = / \/__/  
Universidad Nacional d= e Col. \/__/   \/__/

2008/2/28, soumya s soumya_= samineni * rediffmail.com <owner-chemistry.:.ccl.net>:=

Sent to CCL by: "soumya  s" [soumya_samineni!A!red= iffmail.com]
Hello
It would be nice if some one could suggest a fre= ely available program to build crystals , cut planes and make slabs ..
=
thanx in advance
soumya




------=_Part_1912_3617526.1204207053268-- From owner-chemistry@ccl.net Thu Feb 28 17:50:01 2008 From: "Shikha Varma shikha_-_accelrys.com" To: CCL Subject: CCL: visualisation software in linux Message-Id: <-36383-080228154758-8911-x+HMItjyOYl2w3JCUmPTjg\a/server.ccl.net> X-Original-From: Shikha Varma Content-Type: multipart/alternative; boundary="=_alternative 006EA797882573FD_=" Date: Thu, 28 Feb 2008 12:08:42 -0800 MIME-Version: 1.0 Sent to CCL by: Shikha Varma [shikha|*|accelrys.com] This is a multipart message in MIME format. --=_alternative 006EA797882573FD_= Content-Type: text/plain; charset="US-ASCII" Dear Soumya, Please download the freely available Discovery Studio Visualizer which runs on Linux and performs the tasks you listed. http://accelrys.com/products/discovery-studio/visualization/discovery-studio-visualizer.html Sincerely, Shikha _________________________________ Shikha Varma-O'Brien, Ph.D. Manager, Client Solutions Accelrys, Inc. 10188 Telesis Court, Suite 100 San Diego CA, 92121 Voice: (858)799-5607 Fax: (858)799-5100 e-mail: shikha*accelrys.com http://www.accelrys.com _______________________________________ Accelrys support: 1-800-756-4674 E-mail: support*accelrys.com _______________________________________ "soumya s soumya_samineni * rediffmail.com" Sent by: owner-chemistry*ccl.net 02/28/2008 04:31 AM Please respond to "CCL Subscribers" To "Varma, Shikha " cc Subject CCL: visualisation software in linux Sent to CCL by: "soumya s" [soumya_samineni!A!rediffmail.com] Hello It would be nice if some one could suggest a freely available program to build crystals , cut planes and make slabs .. thanx in advance soumyahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Click on the link below to report this email as spam https://www.mailcontrol.com/sr/d41q9ijf!Wrcohtw78djyfq1jblbDWf9j2ZcGsSMYdQv8aMbHCrH1tUc+LoqES!MxHsOjVk8W1GMuEECkc+4hg== --=_alternative 006EA797882573FD_= Content-Type: text/html; charset="US-ASCII"
Dear Soumya,
Please download the freely available Discovery Studio Visualizer which runs on Linux and performs the tasks you listed.
http://accelrys.com/products/discovery-studio/visualization/discovery-studio-visualizer.html
Sincerely,
Shikha
_________________________________
Shikha Varma-O'Brien, Ph.D.
Manager, Client Solutions
Accelrys, Inc.
10188 Telesis Court, Suite 100
San Diego CA, 92121
Voice: (858)799-5607
Fax: (858)799-5100
e-mail: shikha*accelrys.com
http://www.accelrys.com
_______________________________________
Accelrys support: 1-800-756-4674
E-mail: support*accelrys.com
_______________________________________


"soumya s soumya_samineni * rediffmail.com" <owner-chemistry*ccl.net>
Sent by: owner-chemistry*ccl.net

02/28/2008 04:31 AM
Please respond to
"CCL Subscribers" <chemistry*ccl.net>
To
"Varma, Shikha " <shikha*accelrys.com>
cc
Subject
CCL: visualisation software in linux






Sent to CCL by: "soumya  s" [soumya_samineni!A!rediffmail.com]
Hello
It would be nice if some one could suggest a freely available program to build crystals , cut planes and make slabs ..

thanx in advance
soumya


     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

Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)
     http://www.ccl.net/spammers.txt




--
Click on the link below to report this email as spam
https://www.mailcontrol.com/sr/d41q9ijf!Wrcohtw78djyfq1jblbDWf9j2ZcGsSMYdQv8aMbHCrH1tUc+LoqES!MxHsOjVk8W1GMuEECkc+4hg==

--=_alternative 006EA797882573FD_=-- From owner-chemistry@ccl.net Thu Feb 28 21:53:01 2008 From: "izwan zainurul zainurulizwan80[#]yahoo.com" To: CCL Subject: CCL: Binding energy using CS Chem 3D Pro. Message-Id: <-36384-080227061033-3955-oBn+7qCiFFd0/rWxETUgiQ^server.ccl.net> X-Original-From: izwan zainurul Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-408412678-1204107020=:198" Date: Wed, 27 Feb 2008 02:10:20 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: izwan zainurul [zainurulizwan80]*[yahoo.com] --0-408412678-1204107020=:198 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hai All, I do docking for cyclodextrin with saponin compound using CS Chem 3D Pro. How to calculate binding energy for this complexed using CS Chem 3D Pro. Thanks in advanced. Best wishes, -Izwan. --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-408412678-1204107020=:198 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hai All,
 
I do docking  for cyclodextrin with saponin compound using CS Chem 3D Pro. How to calculate binding energy for this complexed using CS Chem 3D Pro. Thanks in advanced.
 
Best wishes,
-Izwan. 

Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-408412678-1204107020=:198--