From owner-chemistry@ccl.net Fri Aug 26 11:10:34 2005 From: "CCL" To: CCL Subject: CCL: Density Functional Package ADF2005 Released Message-Id: <-29019-050826110126-6157-sJTYeKniThUXNerGpwThRw]*[server.ccl.net> X-Original-From: Stan van Gisbergen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v619.2) Sent to CCL by: Stan van Gisbergen [vangisbergen]*[scm.com] Dear CCL subscribers, The Amsterdam Density Functional package (ADF) is a leading software package for quantum chemistry research using Density Functional Theory (DFT). Strong points include: - many properties and environment models for almost any molecule - excels at transition metal and heavy element compounds. Scientific Computing & Modelling (SCM) proudly announces the release of version ADF2005: * Significant improvements in ADF graphical user interface, more powerful visualization and input builder * Delocalized coordinates and Nudged Elastic Band methods for geometry optimization and transition state search * Faster gradients for large molecules and faster analytic second derivatives (for VWN functional) * Open-shell TDDFT, including spin-flip excitations * Several other enhancements: http://www.scm.com/Doc/Doc2005.01/Background/Updates/page3.html For more information on ADF: * Get a free trial and the ADF brochure from our website http://www.scm.com * Meet us at the ADF workshop at the ACS meeting in Washington next week, or in booth 738. Best regards, Stan van Gisbergen, on behalf of the SCM team. http://www.scm.com E-mail: info]*[scm.com From owner-chemistry@ccl.net Fri Aug 26 11:20:20 2005 From: "CCL" To: CCL Subject: CCL: Software convert 3D structure .sd file to 2D structure Message-Id: <-29020-050826104800-5468-sJTYeKniThUXNerGpwThRw\a/server.ccl.net> X-Original-From: Ferenc Csizmadia Content-Type: multipart/alternative; boundary="------------070406070409050106090101" MIME-Version: 1.0 Sent to CCL by: Ferenc Csizmadia [fcsiz\a/chemaxon.com] This is a multi-part message in MIME format. --------------070406070409050106090101 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit CCL wrote: > Could anybody suggest a software could convert 3D structure file (.sd > or .mol) to a 2D structure file for synthetic chemists reading? > William, MolConverter can output both 2D structure files and 2D images in various formats and can do many other things. Please follow this link http://www.chemaxon.com/marvin/doc/user/molconvert.html for more details. MolConverter is in Java so you can run it on all Java enabled platforms. MolConverter is free if you don't build an application around it (or for academic users: http://www.chemaxon.hu/forum/ftopic193.html) Example, for creating a 2D SDF: $ molconvert sdf *-2* input.sdf -o output.sdf Example, for creating a 2D PNG image of 100x100 pixels: $ molconvert png:w100 *-2* input.mol -o output.png To access MolConverter you need to download the Marvin Beans package (http://www.chemaxon.com/products.html#Marvin), which also includes a structure editor (MarvinSketch), 2D/3D structure viewers (MarvinView, MarvinSpace) and other stuff. Best regards, Ferenc > Thanks in advance, > William > > -------------------------------- > William Wei, Ph.D. > Computational Chemist > Lorus Therapeutics Inc. > 2 Meridian Road > Toronto, On, M9W 4Z7 > 416-798-1200 Ext. 374 > wwei\a/lorusthera.com > > > ------------------------------------------------------------------------ > This message contains CONFIDENTIAL INFORMATION intended solely for the > use of the addressee(s) named above. > Any review, disclosure, distribution, copying or use of the > information by others is strictly prohibited. > If you have received this message in error, please advise the sender > by immediate reply and delete the original message. --------------070406070409050106090101 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit CCL wrote:
Software convert 3D structure .sd file to 2D structure

Could anybody suggest a software could convert 3D structure file (.sd or .mol) to a 2D structure file for synthetic chemists reading?

William,
MolConverter can output both 2D structure files and 2D images in various formats and can do many other things. Please follow this link http://www.chemaxon.com/marvin/doc/user/molconvert.html for more details.
MolConverter is in Java so you can run it on all Java enabled platforms.

MolConverter  is free if you don't build an application around it (or for academic users: http://www.chemaxon.hu/forum/ftopic193.html)

Example, for creating a 2D SDF:
$ molconvert sdf -2 input.sdf -o output.sdf

Example, for creating a 2D PNG image of 100x100 pixels:
$ molconvert png:w100 -2 input.mol -o output.png

To access MolConverter you need to download the Marvin Beans package (http://www.chemaxon.com/products.html#Marvin), which also includes a structure editor (MarvinSketch), 2D/3D structure viewers (MarvinView, MarvinSpace) and other stuff.

Best regards,
Ferenc



Thanks in advance,
William

--------------------------------
William Wei, Ph.D.
Computational Chemist
Lorus Therapeutics Inc.
2 Meridian Road
Toronto, On, M9W 4Z7
416-798-1200 Ext. 374
wwei\a/lorusthera.com


This message contains CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s) named above.
Any review, disclosure, distribution, copying or use of the information by others is strictly prohibited.
If you have received this message in error, please advise the sender by immediate reply and delete the original message.


--------------070406070409050106090101-- From owner-chemistry@ccl.net Fri Aug 26 12:59:02 2005 From: "CCL" To: CCL Subject: CCL: G03 ECP silver atoms Message-Id: <-29022-050826123006-2762-KykjFGgRlvxPvBqImnOjaQ*_*server.ccl.net> X-Original-From: Kirk Peterson Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: Kirk Peterson [kipeters*_*wsu.edu] Specifying an ECP doesn't remove the need to specify a basis set, the ECP just removes your core electrons from the calculation. These are two very different things (although ECPs often are accompanied by a basis set). You need to explicitly input the basis set that goes with the ECP you've chosen. regards, Kirk PS - short plug: new correlation consistent basis sets matched to the accurate ECPs of the Stuttgart/Koeln groups have recently been reported for Cu-Au, Zn-Hg and are available for download from the website given below. -------------------------------------------- Kirk A. Peterson Professor of Chemistry and Materials Science Washington State University Pullman, WA 99164-4630 Office: (509) 335-7867 Fax: (509) 335-8867 kipeters*_*wsu.edu http://tyr0.chem.wsu.edu/~kipeters/ ------------------------------------------------------------------------ On Aug 25, 2005, at 6:02 PM, CCL wrote: > > Sent to CCL by: may abdelghani [may01dz:_:yahoo.fr] > Hello, CCLers > When I decided to constructed a ECP for Ag2 in G03 > software I recognize this problem: in term of this > error message: > QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT > LINE. > > ' > Last state="Top" > TCursr= 879 LCursr= 0 > Error reading general basis specification. > I hop that you can help me to correct my input: > > %chk=Ag2.chk > %mem=6MW > %nproc=1 > # b3pw91 gen pseudo=read test > > Ag2 > > 0 1 > Ag > Ag 1 B1 > > B1 2.68019104 > > Ag 0 > > OLP 3 28 > f > 5 > 0 568.700624 -0.587930000E-01 > 1 162.357907 -20.1145146 > 2 51.1025755 -104.273311 > 2 16.9205822 -40.4539787 > 2 6.16695960 -3.44200090 > s-f > 5 > 0 76.0974658 2.98615270 > 1 15.3327359 35.1576460 > 2 18.7715345 450.180991 > 2 13.3663294 -866.024831 > 2 9.82369480 523.111018 > p-f > 5 > 0 56.3318043 4.96406710 > 1 69.0609098 21.5028219 > 2 19.2717998 546.027545 > 2 12.5770654 -600.382256 > 2 8.79566700 348.294929 > d-f > 5 > 0 53.4641078 3.04674860 > 1 40.1975457 23.3656705 > 2 11.9086073 777.254012 > 2 9.75281830 -1238.86024 > 2 8.17889970 608.067712 > > > > > > > > _______________________________________________________________________ > ____ > Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! > Messenger > Téléchargez cette version sur http://fr.messenger.yahoo.com> To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST*_*ccl.net> > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > From owner-chemistry@ccl.net Fri Aug 26 12:58:42 2005 From: "CCL" To: CCL Subject: CCL: Castep-PDOS Message-Id: <-29021-050826122915-2372-KykjFGgRlvxPvBqImnOjaQ|-|server.ccl.net> X-Original-From: George Fitzgerald Content-Type: multipart/alternative; boundary="=_alternative 0056204588257069_=" MIME-Version: 1.0 Sent to CCL by: George Fitzgerald [gxf|-|accelrys.com] This is a multipart message in MIME format. --=_alternative 0056204588257069_= Content-Type: text/plain; charset="US-ASCII" Dear Serdar, If you are using the latest version of CASTEP, you can plot band structures, DOS, orbitals, and electrostatic potentials using the Accelrys Materials Studio interface. For details on the procedure, you should contact Accelrys support at support|-|accelrys.com. If you don't have a copy of the interface, then please contact me directly. Sincerely, george ____________________________________________ George Fitzgerald, Ph.D. gxf|-|accelrys.com Accelrys, Inc. Tel: +1 858 799 5360 10188 Telesis Court Fax: +1 858 799 5100 Suite 100 Mobile: +1 858 692 8722 San Diego, CA 92121 "CCL" Sent by: owner-chemistry|-|ccl.net 08/25/2005 10:43 AM Please respond to "CCL Subscribers" To "Fitzgerald, George " cc Subject CCL: Castep-PDOS Sent to CCL by: "serdar durdagi" [durdagi]|[fhi-berlin.mpg.de] Hi, In my calculations, I am using CASTEP. Does anybody knows, how can I plot PDOS from pdos_weights file. It is a binary file. Thank you very much. Serdar Durdagi -------------------------------------------------- Serdar Durdagi, M.Sc. Ph.D. student Theory Department, Fritz-Haber-Institute of Max-Planck Society Faradayweg, 4-6, Berlin-Dahlem, D-14195,Germany Tel: +49-30-8413-4844 (office) +49-162-201-3631 (mobile) -------------------------------------------------- --=_alternative 0056204588257069_= Content-Type: text/html; charset="US-ASCII"
Dear Serdar,

If you are using the latest version of CASTEP, you can plot band structures, DOS, orbitals, and electrostatic potentials using the Accelrys Materials Studio interface. For details on the procedure, you should contact Accelrys support at support|-|accelrys.com. If you don't have a copy of the interface, then please contact me directly.

Sincerely,
george
____________________________________________
George Fitzgerald, Ph.D.       gxf|-|accelrys.com
Accelrys, Inc.                             Tel:  +1 858 799 5360
10188 Telesis Court                 Fax: +1 858 799 5100
Suite 100                                     Mobile: +1 858 692 8722
San Diego, CA 92121


"CCL" <owner-chemistry|-|ccl.net>
Sent by: owner-chemistry|-|ccl.net

08/25/2005 10:43 AM
Please respond to
"CCL Subscribers" <chemistry|-|ccl.net>
To
"Fitzgerald, George " <gxf|-|accelrys.com>
cc
Subject
CCL: Castep-PDOS






Sent to CCL by: "serdar durdagi" [durdagi]|[fhi-berlin.mpg.de]
Hi,

In my calculations, I am using CASTEP. Does anybody knows, how can I plot
PDOS from pdos_weights file. It is a binary file.

Thank you very much.

Serdar Durdagi

--------------------------------------------------
Serdar Durdagi, M.Sc.
Ph.D. student
Theory Department,
Fritz-Haber-Institute of Max-Planck Society
Faradayweg, 4-6, Berlin-Dahlem, D-14195,Germany
Tel: +49-30-8413-4844 (office)
    +49-162-201-3631 (mobile)
--------------------------------------------------
--=_alternative 0056204588257069_=-- From owner-chemistry@ccl.net Fri Aug 26 12:59:25 2005 From: "CCL" To: CCL Subject: CCL: CCL question about limitations of PCM Message-Id: <-29023-050826114537-31637-KykjFGgRlvxPvBqImnOjaQ#%#server.ccl.net> X-Original-From: khunter#%#mta.ca Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 MIME-Version: 1.0 Sent to CCL by: khunter#%#mta.ca We are investigating a transition state of a proton transfer mechanism. We successfully modelled such a state in the gas phase and are now looking at the solvation effects using the PCM method. However, the transfering hydrogen is unbound (according to the gas phase) and upon trying to do a solvation calculation we receive the following error. United Atom Topological Model (UA0 parameters set). UA0: Hydrogen 21 is unbound. Keep it explicit at all point on the UA0: potential energy surface to get meaningful results. Is this error a limitation of the PCM or does anyone have advice on how to correct this error? Any assistance would be greatly appreaciated. From owner-chemistry@ccl.net Fri Aug 26 16:25:22 2005 From: "CCL" To: CCL Subject: CCL: Molecular dynamics w/ 2D PBC Message-Id: <-29024-050826162421-4905-KykjFGgRlvxPvBqImnOjaQ:-:server.ccl.net> X-Original-From: Aaron Deskins Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed MIME-Version: 1.0 Sent to CCL by: Aaron Deskins [ndeskins:-:purdue.edu] CCL wrote: >Sent to CCL by: Rick Venable [rvenable]|[pollux.cber.nih.gov] >On Thu, 25 Aug 2005, CCL wrote: > > > >Since the question topic was "molecular dynamics" I was assuming a >package such as CHARMM, AMBER, NAMD, GROMOS, TINKER, etc., most of which >do fairly well at describing periodic structures, esp. for the 3D case. >Details such as system height, slab thickess, etc. would need to be >optimized, but it's a reasonable option, esp. if 2D PBC aren't readily >available. OTOH, the water:gold interaction might be tricky to get >right with a simple point charge based potential; a polarizable >potential might be a better choice. > > > Thank you for the response. If it's not too much trouble, perhaps you (or any CCL reader) could give a sample article(s)/review to look up on using some of the more well-known empirical programs to model metal surfaces and especially adsorbate/surface systems. Thank you again, Aaron Deskins Purdue University