From owner-chemistry@ccl.net Mon Mar 30 05:30:01 2015 From: "Syeda Sumayya Tariq sumayyatariq7|-|gmail.com" To: CCL Subject: CCL: Can you help me with a HADDOCK error concerning distance restraints? Message-Id: <-51204-150330052706-27560-ABhcrPLlDGtgWllI+8VTkA,+,server.ccl.net> X-Original-From: "Syeda Sumayya Tariq" Date: Mon, 30 Mar 2015 05:27:04 -0400 Sent to CCL by: "Syeda Sumayya Tariq" [sumayyatariq7() gmail.com] Hi Everyone, I have recently started working with HADDOCK stand alone and am facing some trouble running it. I wonder if anyone of you could help me in this regard. I started with separating the 2 proteins in PDB ID: 1L4Z, and then docking them with HADDOCK 2.1. But it is giving me the following error, TOTAL NUMBER OF DISTANCE RESTRAINTS FOR RIGID BODY DOCKING IS ZERO! CONTROL YOUR PARAMETER SETTINGS AND RESTRAINT DEFINITIONS STRUCTURE NUMBER 1 I have set up the Upper distance limit for AIRs as 2.0 when generating the air.tbl file and all the other restraints as default in the run.cns file. I know it may be a naive question but please consider that I am new to this field. Any help would be highly appreciated. From owner-chemistry@ccl.net Mon Mar 30 09:50:01 2015 From: "Jim Kress jimkress35 * gmail.com" To: CCL Subject: CCL: Is there any online resources for DFT studies on small molecules Message-Id: <-51205-150330094444-11559-U1QNPVXEjeDITiM2wRvXCg * server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 Mar 2015 09:44:38 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35]|[gmail.com] Firefly, ORCA, GAMESS, NWChem, ADF, Q-Chem - just to name a few. The first 4 are available for no charge. Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com|a|ccl.net [mailto:owner-chemistry+jimkress35==gmail.com|a|ccl.net] On Behalf Of Mannan K malie_03- -yahoo.co.in Sent: Sunday, March 29, 2015 11:06 PM To: Kress, Jim Subject: CCL: Is there any online resources for DFT studies on small molecules Sent to CCL by: "Mannan K" [malie_03,+,yahoo.co.in] Dear All, I would like to perform DFT studies on small molecules prior to docking study to obtain optimized structure. Is there any free or online resources available for performing DFT studies on small molecules. Many Thanks, Mannanhttp://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 Mon Mar 30 11:48:00 2015 From: "Safiya Ess Amer amersaf85- -yahoo.com" To: CCL Subject: CCL:G: Ghost atoms (symbol Bq) Message-Id: <-51206-150330114329-16279-l5oLo9itXFejfOI0sVxG8w-*-server.ccl.net> X-Original-From: "Safiya Ess Amer" Date: Mon, 30 Mar 2015 11:43:27 -0400 Sent to CCL by: "Safiya Ess Amer" [amersaf85__yahoo.com] > "Eduardo edulsa()ufpr.br" wrote: > > Sent to CCL by: Eduardo [edulsa/a\ufpr.br] > Dear Safiya > > > Sent to CCL by: "Safiya Ess Amer" [amersaf85||yahoo.com] > > Hello. > > Please, how can I use ghost atom with Cartesian coordinates? > > I have system of H2-Fe(OH)3 and use G03W for getting energy as function of > > more distances (Z) from center of H2 to Fe atom. I am calculating now each > > value of energy at some distance manually. I need to put ghost atom at center > > of H2, how can I do that to get PES. > > > > Can anyone help me in input file? > > I have geometry of the system. > > > > Thanks in advance > > > > Safiya Amer > > amersaf85]^[yahoo.com > > > > > I used ghost atoms a long time ago, but if I can remember, the symbol > for it is "X" instead "Bq". > > Cheers > > Eduardo> > > > Thanks to reply Eduardo I know that the symbol for ghost atoms is "Bq" and for dummy atoms is "X", but I don not know what > is the different between them? when you have the answer please tell me. Safiya Amer Graduate student From owner-chemistry@ccl.net Mon Mar 30 18:34:01 2015 From: "Gutsev, Gennady L. gennady.gutsev(~)famu.edu" To: CCL Subject: CCL:G: Ghost atoms (symbol Bq) Message-Id: <-51207-150330173734-27636-/o+jTBLj4uZWCQoCcz5jMg[]server.ccl.net> X-Original-From: "Gutsev, Gennady L." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 30 Mar 2015 21:37:25 +0000 MIME-Version: 1.0 Sent to CCL by: "Gutsev, Gennady L." [gennady.gutsev-$-famu.edu] Dear Safiya: A dummy X "atom" is used in Z-matrix constructions. For example, let us take a linear M3 trimer. Its Z-matrix can be written as M X 1 10.0 M 1 r1 2 90.0 M 1 r2 2 90.0 3 180.0 r1=... r2=... The value of 10.0 is arbitrary; the role of the X dummy is to build a linear structure. A Bq "atom" is used to indicate the position of a point where an additional basis set is to be placed. It can be used, for example, in placing at the Bq position of very diffuse functions in computations of dipole-bound states of anions whose neutral parents possess a large (> 2.5 Debye) dipole moments. The Bq "atoms" are also used in counterpoise computations. Z-nmatrix would be: M Bq 1 Rq M 1 r1 2 90.0 M 1 r2 2 90.0 3 180.0 r1=... r2=... Rq=3.0 If to remove an empty line between "r2" and "Rq", then Rq will also be optimized which is generally unneccessaraly. In this case use the GEN basis description. Good luck, Gennady Gutsev ________________________________________ > From: owner-chemistry+gennady.gutsev==famu.edu*_*ccl.net on behalf of Safiya Ess Amer amersaf85- -yahoo.com Sent: Monday, March 30, 2015 11:43 AM To: Gutsev, Gennady L. Subject: CCL:G: Ghost atoms (symbol Bq) Sent to CCL by: "Safiya Ess Amer" [amersaf85__yahoo.com] > "Eduardo edulsa()ufpr.br" wrote: > > Sent to CCL by: Eduardo [edulsa/a\ufpr.br] > Dear Safiya > > > Sent to CCL by: "Safiya Ess Amer" [amersaf85||yahoo.com] > > Hello. > > Please, how can I use ghost atom with Cartesian coordinates? > > I have system of H2-Fe(OH)3 and use G03W for getting energy as function of > > more distances (Z) from center of H2 to Fe atom. I am calculating now each > > value of energy at some distance manually. I need to put ghost atom at center > > of H2, how can I do that to get PES. > > > > Can anyone help me in input file? > > I have geometry of the system. > > > > Thanks in advance > > > > Safiya Amer > > amersaf85]^[yahoo.com > > > > > I used ghost atoms a long time ago, but if I can remember, the symbol > for it is "X" instead "Bq". > > Cheers > > Eduardo> > > > Thanks to reply Eduardo I know that the symbol for ghost atoms is "Bq" and for dummy atoms is "X", but I don not know what > is the different between them? when you have the answer please tell me. Safiya Amer Graduate studenthttp://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 Mon Mar 30 19:14:00 2015 From: "Yingbin Ge yingbin.ge#%#gmail.com" To: CCL Subject: CCL:G: Ghost atoms (symbol Bq) Message-Id: <-51208-150330191121-10339-quXDoKIT0lD9i1OBw+XIBg]![server.ccl.net> X-Original-From: Yingbin Ge Content-Type: multipart/alternative; boundary=001a11475844412e1d0512899900 Date: Mon, 30 Mar 2015 16:11:14 -0700 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge#gmail.com] --001a11475844412e1d0512899900 Content-Type: text/plain; charset=UTF-8 Dear Safiya Amer, Dummy atoms have no charge, no mass, no basis functions. Dummy atoms are often used to construct a structure using z-matrix. You may find the following web page useful: http://www.gaussian.com/g_tech/g_ur/c_zmat.htm . Ghost atoms may have an arbitrary charge, may have an arbitrary mass (please double check on this), may act as the centers of an arbitrary set of basis functions. Ghost atoms are often used to add point charges to the system or used to calculate approximately the basis set superposition errors (BSSE). You may find this web page useful: http://www.gaussian.com/g_tech/g_ur/k_counterpoise.htm . Neither dummy atoms nor ghost atoms are real atoms. I apologize for confusing dummy atoms with ghost atoms a few days ago. Sincerely, Yingbin Yingbin Ge, Associate Professor Science Building 207A Department of Chemistry Central Washington University 400 E University Way Ellensburg, WA 98926 Office Phone: 509-963-2817 Email: yingbin|*|cwu.edu --001a11475844412e1d0512899900 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Safiya Amer,

Dummy atoms = have no charge, no mass, no basis functions.
Dummy atoms are often used= to construct a structure using z-matrix. You may find the following web pa= ge useful: http:= //www.gaussian.com/g_tech/g_ur/c_zmat.htm .

Ghost atoms ma= y have an arbitrary charge, may have an arbitrary mass (please double check= on this), may act as the centers of an arbitrary set of basis functions.
Ghost atoms are often used to add point charges to the system = or used to calculate approximately the basis set superposition errors (BSSE= ). You may find this web page useful: http://www.gaussian.com/g_tech/g_ur/k_counter= poise.htm .


Neither dummy atoms nor gh= ost atoms are real atoms.

I apologize for confusing dummy atoms wit= h ghost atoms a few days ago.

Sincerely,
Yingbin=


Yingbin Ge, Associate Professor
Science Building 207A
Department of Chemistry
Central Washington University
400 E University Way
Ellensburg, WA 98926
Office Phone: 509-963-2817
Email: yingbin|*|cwu.edu=
--001a11475844412e1d0512899900-- From owner-chemistry@ccl.net Mon Mar 30 21:52:00 2015 From: "Muhammad Khattab muhammadkhattab++hotmail.com" To: CCL Subject: CCL: Gaussian09 Message-Id: <-51209-150330212802-28854-H6EdebuzLA16BOgi+aSimw- -server.ccl.net> X-Original-From: "Muhammad Khattab" Date: Mon, 30 Mar 2015 21:28:00 -0400 Sent to CCL by: "Muhammad Khattab" [muhammadkhattab~!~hotmail.com] Hello, I am a beginner in using G09, and I appreciate if yo could send me name of resources for better understanding of G09, specially in UV-Vis, freezing a bond, excited states and solvatochromism. Sincerely, Muhammad Khattab PhD Scholar Cell Biophysics Laboratory (Centre for Micro-Photonics) Molecular Model Discovery Laboratory (Chemistry & Biotechnology Dept.) Faculty of Science, Engineering and Technology Swinburne University of Technology Hawthorn, Melbourne, Victoria 3122, Australia Email: muhammadkhattab---hotmail.com Mobile: (+61) 0403588905