From owner-chemistry@ccl.net Tue Dec 29 09:30:00 2009 From: "mzhy1019..sina.com" To: CCL Subject: CCL: Isolated molecules & unoccupied orbitals: does the basis set matter? Message-Id: <-40974-091229092417-29709-siH81eFg5pAGZjp6ZWyjxA%%server.ccl.net> X-Original-From: mzhy1019.%%.sina.com Content-Type: multipart/alternative; boundary="=-sinamail_alt_732fcd48d37198787acc044a9e173aba" Date: Tue, 29 Dec 2009 22:19:52 +0800 MIME-Version: 1.0 Sent to CCL by: mzhy1019 * sina.com --=-sinamail_alt_732fcd48d37198787acc044a9e173aba Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: base64 Content-Disposition: inline CkRlYXIgVWxmLAoKVGhhbmtzIGEgbG90IGZvciB5b3VyIHJlcGx5IQoKSSBpbmNyZWFzZWQNCnRo ZSBiYXNpcyBzZXQgKDYtMzFHKiopIGJ5IGFkZGluZyBkaWZmdXNlIGZ1bmN0aW9ucyBpbiBHYXVz c2lhbjAzDQpzb2Z0d2FyZSwgdG8gKDYtMzErK0cqKikuIFRoZSBET1MgcmVzdWx0cyBzaG93IHRo YXQgdGhlIFVOT0NDVVBJRUQNCnN0YXRlcyBhcmUgbGFyZ2VseSBjaGFuZ2VkIGJvdGggaW4gZW5l cmd5IGFuZCBtYWduaXRpdHVkZS4gV2UgYWxzbw0KZm91bmQgdGhhdCB0aGUgYmFuZGdhcCB3YXMg ZXhwYW5kZWQsIGFuZCBpbiBjb250cmFzdCB0byB0aGUgZm9ybWVyDQpjYWxjdWxhdGlvbiwgdGhl IE9DQ1VQSUVEIHN0YXRlcyBkaWRuJ3QgbWF0Y2ggdGhlIHBsYW5lLXdhdmUgcmVzdWx0DQp3ZWxs IGFueW1vcmUsIGluIHRoaXMgc2Vuc2Ugd2UgY2FuIG5vdCBpbW1lZGlhdGVseSBzZWUgdGhhdCB0 aGUgcmVzdWx0DQp3aXRoIGRpZmZ1c2UgYmFzaXMgZnVuY3Rpb25zIGZpdHMgdGhlIHBsYW5lLXdh dmUgY29kZXMgYmV0dGVyLgoKVGhlbiBsZXQgdXMgc2VlIG15IG9yaWdpbmFsIHF1ZXN0aW9uIGFn YWluOgoKSQ0KZm9jdXNlZCBvbiB0aGUgbW9sZWN1bGUgNC1QeXJpZGluLTQteWwtcGhlbnlsYW1p bmUuIFVzaW5nIFNpZXN0YQ0KKGxvY2FsLWJhc2lzLXNldCBjb2RlKSwgSSBzZWUgNCB1bm9jY3Vw aWVkIHN0YXRlcyBiZWxvdyB0aGUgdmFjdXVtDQplbmVyZ3kgKCJWYWNFbiIpIGluIERPUyBzcGVj dHJ1bTogCgouLi4gSE9NTyBMVU1PIEwrMSBMKzImbmJzcDsmbmJzcDsmbmJzcDsgTCszIFZhY0Vu IEwrNCAuLi4KClRoZW4NCnBlcmZvcm1pbmcgVkFTUCAocGxhbmUtd2F2ZSBjb2RlKSBjYWxjdWxh dGlvbnMgb24gdGhlIHNhbWUgbW9sZWN1bGUsDQp0aGUgRE9TIG1hdGNoZXMgdGhvc2Ugc3RhdGVz IHZlcnkgbmljZWx5IHVwIHRvIHRoZSBMKzIsIHdob3NlDQozRC1yZXByZXNlbnRhdGlvbnMgb2Yg dGhlIG9yYml0YWxzIGFyZSBjb25zaXN0ZW50IGFzIHdlbGwuIEJldHdlZW4gdGhlDQpzdGF0ZXMg TCsyIGFuZCBMKzMgKGFjY29yZGluZyB0byBTaWVzdGEpLCBWQVNQIGNhbGN1bGF0ZXMgYW4gYWRk aXRpb25hbA0Kc3RhdGUgKCJleCIpLiBCeSBsb29raW5nIGF0IGl0cyAzRC1yZXByZXNlbnRhdGlv biwgSSBjYW4gc2VlIHRoYXQgdGhpcw0Kc3RhdGUgbG9va3MgbGlrZSB3aGF0IGlzIHRoZSBMKzQg KHRoZSBmaXJzdCBzdGF0ZSBhYm92ZSB0aGUgdmFjdXVtDQplbmVyZ3kpIGluIFNpZXN0YTsgU28g dGhpcyBvcmJpdGFsIGlzIG5vdCBtaXNzaW5nIGluIGxvY2FsIGJhc2lzLXNldA0KY2FsY3VsYXRp b24hIEZ1cnRoZXIsIGNvbXBhcmluZyB0aGUgM0QgcmVwcmVzZW50YXRpb25zIG9mIHRoZSBMKzMg c3RhdGUNCmluIHRoZSB0d28gY29kZXMsIEkgZG9uJ3QgdGhpbmsgdGhleSByZXByZXNlbnQgdGhl IHNhbWUgb3JiaXRhbC4KCi4uLiBIT01PIExVTU8gTCsxIEwrMiBleCBMKzMgVmFjRW4KCkJhc2Vk DQpvbiB0aGUgYWJvdmUsIG15IG1haW4gcHJvYmxlbSBpczogSW4gcGxhbmUtd2F2ZSBhbmQgbG9j YWwtYmFzaXMgc2V0DQpjb2Rlcywgd2h5IHdlIGNhbiBzZWUgdGhlIHNhbWUgdW5vY2N1cGllZCBv cmJpdGFscyAoaS5lLiAiTCs0IiBpbg0KU2llc3RhIGFuZCAiZXgiIGluIFZBU1ApIGF0IGRpZmZl cmVudCBlbmVyZ3kgcG9zaXRpb25zPyBBbmQgbW9zdA0KaW1wb3J0YW50bHk6IHdoaWNoIGNvZGUg aXMgcmlnaHQ/CgoKU2luY2VyZWx5LApaaG9uZ3l1bgpJbnN0aXR1dGUgb2YgY2hlbWlzdHJ5LCBD aGluZXNlIEFjYWRlbXkgb2YgU2NpZW5jZXMKCj4gIFllcywgYmVjYXVzZSB0aGVzZSAoflJ5ZGJl cmcpIG9yYml0YWxzIGNhbiBiZSB2ZXJ5IHZlcnkgbGFyZ2UsIGFuZCBhcmUKPiAgdHlwaWNhbGx5 IG5vdCBpbmNsdWRlZCBpbiBzdGFuZGFyZCBiYXNpcyBzZXRzLiBJbiB0aGlzIHNlbnNlIHRoZSBw bGFuZQo+ICB3YXZlIGJhc2lzIGlzIGJldHRlciwgdW50aWwgeW91IGhpdCB0aGUgYm91bmRhcnkg b2YgeW91ciB1bml0IGNlbGwuIFlvdQo+ICBkb24ndCBtZW50aW9uIHdoaWNoIGJhc2lzIHNldCB5 b3UgdXNlLCBidXQgaWYgeW91IHRyeSB0byBpbmNyZWFzZSBpdCBieQo+ICBhZGRpbmcgbW9yZSBk aWZmdXNlIGZ1bmN0aW9ucyAoc29tZSBwcm9ncmFtcyBjYW4gZG8gdGhpcyBhdXRvLQo+ICBtYXRp Y2FsbHkpIHlvdSB3aWxsIG1vc3QgbGlrZWx5IGZpbmQgeW91ciBwbGFuZSB3YXZlIHN0YXRlcyBh bHNvIGluIHlvdXIKPiAgbG9jYWxpemVkIG9yYml0YWwgY2FsY3VsYXRpb25zLiBJdCBjYW4gaGFw cGVuIHRoYXQgeW91ciBzdGF0ZSB0aGF0IGlzIHRvbwo+ICBoaWdoIHdpdGggdGhlIHNtYWxsIGJh c2lzIHdpbGwgY29tZSBkb3duIGluIGVuZXJneSB3aXRoIGEgbW9yZQo+ICBhcHByb3ByaWF0ZSBi YXNpcy4KPiAgU2luY2VyZWx5LAo+ICBVbGYgRWtzdHLDtm0sIFZVIFVuaXZlcnNpdHkgQW1zdGVy ZGFtLg== --=-sinamail_alt_732fcd48d37198787acc044a9e173aba Content-Type: text/html; 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charset=ISO-8859-1 Date: Mon, 28 Dec 2009 08:32:22 -0800 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt__gmail.com] Also check out Avogadro (http://avogadro.sf.net). It's open-source and has binaries for a variety of platforms. Adam On Sun, Dec 27, 2009 at 7:04 AM, Narendra Revanuri vyasa.naren::gmail.com wrote: > HI, You can try chemcraft(you can download Trial version) , you can creat= e > desired molecule and corresponding XYZ=A0coordinates=A0can be copied or y= ou also > have an option of saving the file in xyz format > > Regards > Naren > On Sat, Dec 26, 2009 at 5:04 PM, Taye Beyene Demissie sene3095(-)yahoo.co= m > wrote: >> >> Sent to CCL by: "Taye Beyene Demissie" [sene3095() yahoo.com] >> Hello CCL members? Merry Christmas! >> I want to generate xyz input file for my molecules which I will use them >> for calculations on molden, gaussian and PCmodel. How can I generate thi= s >> xyz coordinate input file? I tried it on molden but it is not working >> properly and it will not give the correct 3-D orientation. It may be my >> problem. >> Thank you for your help in advance. >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY{}ccl.net or use: >> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message >> >> E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net or use >> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message>> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml>> =A0 =A0 =A0http://www.ccl.net/spammers.txt>> >> > > From owner-chemistry@ccl.net Tue Dec 29 10:39:01 2009 From: "meera chawla meera_._seascapelearning.com" To: CCL Subject: CCL: Symposium on Shape and Electrostatics in Drug Discovery in India Message-Id: <-40976-091229022743-11953-INQ7zZNhrbIAsRuWdxZAvA a server.ccl.net> X-Original-From: meera chawla Content-Type: multipart/alternative; boundary="------------090607010200030704060001" Date: Mon, 28 Dec 2009 22:26:15 -0800 MIME-Version: 1.0 Sent to CCL by: meera chawla [meera__seascapelearning.com] This is a multi-part message in MIME format. --------------090607010200030704060001 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Seascape Learning, in collaboration with OpenEye Scientific, and Indian Scientific Experts from (JNU-New Delhi and, GVKBio-Hyderabad) is pleased to offer an Interactive Symposium on Shape and Electrostatics Best Practices for Virtual Screening and Lead-Hopping in Drug Discovery Research. The dates and locations of the symposium are as follows: JNU-New Delhi - 28 and 29 Jan 2010 GVKBio - Hyderabad: 3 & 4 Feb 2010 For details, including registration, please visit www.seascapelearning.com/oe_symp Regards Meera ps: This is a Seascape educational initiative with all proceeds going to support education in India. --------------090607010200030704060001 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit
Seascape Learning, in collaboration with OpenEye Scientific, and Indian Scientific Experts from (JNU-New Delhi and, GVKBio-Hyderabad) is pleased to offer an Interactive Symposium on Shape and Electrostatics Best Practices for Virtual Screening and Lead-Hopping in Drug Discovery Research.

The dates and locations of the symposium are as follows:

JNU-New Delhi – 28 and 29 Jan 2010
GVKBio – Hyderabad: 3 & 4 Feb 2010

For details, including registration, please visit www.seascapelearning.com/oe_symp

Regards

Meera
ps: This is a Seascape educational initiative with all proceeds going to support education in India. --------------090607010200030704060001-- From owner-chemistry@ccl.net Tue Dec 29 14:31:01 2009 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= uekstrom ~~ gmail.com" To: CCL Subject: CCL:G: Isolated molecules & unoccupied orbitals: does the basis set matter? Message-Id: <-40977-091229105818-26365-Y5+oUadUOy67oy/c9PuRrg_-_server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 29 Dec 2009 16:58:06 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [uekstrom]~[gmail.com] Dear Zhongyun, can I ask you what meaning you want to assign to the virtual orbitals? When you are near the vacuum level there is an infinite number (in an exact basis) of states in any given energy range. Therefore it's very diffi= cult to use these states for interpretation. You should rather calculate some observable property using time dependent density functional theory (or similar). > I increased the basis set (6-31G**) by adding diffuse functions in > Gaussian03 software, to (6-31++G**). The DOS results show that the > UNOCCUPIED states are largely changed both in energy and magnititude. That is to be expected. > We > also found that the bandgap was expanded, and in contrast to the former > calculation, the OCCUPIED states didn't match the plane-wave result well > anymore, in this sense we can not immediately see that the result with > diffuse basis functions fits the plane-wave codes better. This is strange, the diffuse functions should not have any effect on the occupies states if your 6-31G** basis was sufficient in the first place. > Based on the above, my main problem is: In plane-wave and local-basis set > codes, why we can see the same unoccupied orbitals (i.e. "L+4" in Siesta = and > "ex" in VASP) at different energy positions? And most importantly: which > code is right? I would guess that the plane wave code is "right". But you should be very careful with giving meaning to these virtual states, and make sure that your result= s are converged with respect to the basis set (or plane wave cutoff energy and k-= space integration grid). I am sorry that I cannot give a more detailed answer, I do not have a lot of experience with periodic calculations of this type. I have been computing Rydberg states for small molecules, in that case I use a large (20s20p20d) basis set just for these states, from which I can get up to n=3D10 or so. Sincerely, Ulf Ekstr=F6m, VU University Amsterdam.