From owner-chemistry@ccl.net Fri Apr 11 00:17:01 2008 From: "Guanna Li gnli/./dicp.ac.cn" To: CCL Subject: CCL: theory relate to circular dichroism sepctrum (ECD) Message-Id: <-36697-080410214201-16533-uJ3bEazzPt7Q5faL5m7DeA[*]server.ccl.net> X-Original-From: "Guanna Li" Content-Transfer-Encoding: base64 Content-Type: text/plain; charset="gb2312" Date: Fri, 11 Apr 2008 09:40:39 +0800 Mime-Version: 1.0 Sent to CCL by: "Guanna Li" [gnli]|[dicp.ac.cn] RGVhciAgQ0NMZXIsDQpJIGdvdCBteSBmaXJzdCBzZW1pbmFyIHRpdGxlICd0aGVvcnkgYW5kIGV4 cGVyaW1lbnQgb2YgY2lyY3VsYXIgZGljaHJvaXNtIHNwZWN0cnVtIChDRCkno6yjyWRvd25sb2Fk IHNvbWUgYXJ0aWNsZXMgYnV0IG1vc3Qgb2YgdGhlbSBpcyBhYm91dCBleHBlcmltZW50YWwgYW5k IGRmdCBjYWxjdWxhdGUgcmVzdWx0Lg0KdGhleSBhcmUgaGFyZGx5IHJlZmVyIHRvIHRoZSBiYXNp YyB0aGVvcnkgb2YgQ0QgaW4gdGhlIGludHJvZHVjdGlvbiBvciB0aGVvcnkgcGFydC4NCkkgd2ls bCB2ZXJ5IGFwcHJlY2lhdGUgaWYgYW55b25lIGNhbiByZWNvbW1lbmQgc29tZSBwYXBlciBhYm91 dCB0aGUgdGhlb3J5IG9mIENEIGZvciBtZS4NClRoYW5rIHlvdSAhDQogCQkJCQ0KQmVzdCB3aXNo ZXMgDQpHdWFubmEgTGkNCkVtYWlsOiBnbmxpQGRpY3AuYWMuY24NCg== From owner-chemistry@ccl.net Fri Apr 11 01:45:00 2008 From: "Arthur computationalboy|a|gmail.com" To: CCL Subject: CCL: protein-ligand docking software Message-Id: <-36698-080410094313-27799-4SIkQgTnrMuCjQ9ThXSLHg-.-server.ccl.net> X-Original-From: "Arthur" Content-Type: multipart/alternative; boundary="----=_NextPart_08041019465673444207007_002" Date: Thu, 10 Apr 2008 19:47:03 +0800 MIME-Version: 1.0 Sent to CCL by: "Arthur"[computationalboy[A]gmail.com] ------=_NextPart_08041019465673444207007_002 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 SGksRmxleHhHVUkgYW5kIE1vbGVncm8gVmlydHVhbCBEb2NrZXIgaXMgcXVpdGUgZnJpZW5kbHkg d2l0aCBoaWdoIGFjY3VyYWN5Lg0KVGhleSBvZmZlciBhIHBlcmlvZCBvZiBldmFsdWF0aW9uLg0K DQpFbmpveSENCg0KQXJ0aHVyLCBjb21wdXRhdGlvbmFsYm95QGdtYWlsLmNvbQ0KMjAwOC0wNC0x MCANCi0tLS0tIFJlY2VpdmluZyB0aGUgZm9sbG93aW5nIGNvbnRlbnQgLS0tLS0gDQpGcm9tOiBI YXRpY2UgQ2FuIGFscGhhY2FuMjAwMF8uX3lhaG9vLmNvbSANClJlY2VpdmVyOiBXYW5nLEppYW4g LWlkIzRuMy0gDQpUaW1lOiAyMDA4LTA0LTEwLCAxNjowNjo0OA0KU3ViamVjdDogQ0NMOiBwcm90 ZWluLWxpZ2FuZCBkb2NraW5nIHNvZnR3YXJlDQoNCg0KU2VudCB0byBDQ0wgYnk6ICJIYXRpY2Ug Q2FuIiBbYWxwaGFjYW4yMDAwIC4uIHlhaG9vLmNvbV0NCkRlYXIgQWxsLA0KDQpJIHdvdWxkIGJl IHZlcnkgZ3JhdGVmdWwgZm9yIHBvaW50ZXJzL2FkdmlzZSBldGMgb24NCmVzcGVjaWFsbHkgdXNl ci1mcmllbmRseSBzb2Z0d2FyZSBhbmQgcmV2aWV3cy9saXRlcmF0dXJlIHN1aXRhYmxlIGZvciBh DQpuZXdjb21lciB0byBtb2xlY3VsYXIgZG9ja2luZyAocHJvdGVpbi9wcm90ZWluLywgcHJvdGVp bi9saWdhbmQpLg0KDQpNYW55IHRoYW5rcyBhbmQga2luZCByZWdhcmRzDQoNCkhhdGljZQ0KDQoN Cg0KLT0gVGhpcyBpcyBhdXRvbWF0aWNhbGx5IGFkZGVkIHRvIGVhY2ggbWVzc2FnZSBieSB0aGUg bWFpbGluZyBzY3JpcHQgPS0NClRvIHJlY292ZXIgdGhlIGVtYWlsIGFkZHJlc3Mgb2YgdGhlIGF1 dGhvciBvZiB0aGUgbWVzc2FnZSwgcGxlYXNlIGNoYW5nZQ0KdGhlIHN0cmFuZ2UgY2hhcmFjdGVy cyBvbiB0aGUgdG9wIGxpbmUgdG8gdGhlIEAgc2lnbi4gWW91IGNhbiBhbHNvDQpsb29rIHVwIHRo ZSBYLU9yaWdpbmFsLUZyb206IGxpbmUgaW4gdGhlIG1haWwgaGVhZGVyLg0KDQpFLW1haWwgdG8g c3Vic2NyaWJlcnM6IENIRU1JU1RSWUBjY2wubmV0IG9yIHVzZToNCiAgICAgIGh0dHA6Ly93d3cu Y2NsLm5ldC9jZ2ktYmluL2NjbC9zZW5kX2NjbF9tZXNzYWdlDQoNCkUtbWFpbCB0byBhZG1pbmlz dHJhdG9yczogQ0hFTUlTVFJZLVJFUVVFU1RAY2NsLm5ldCBvciB1c2UNCiAgICAgIGh0dHA6Ly93 d3cuY2NsLm5ldC9jZ2ktYmluL2NjbC9zZW5kX2NjbF9tZXNzYWdlDQoNClN1YnNjcmliZS9VbnN1 YnNjcmliZTogDQogICAgICBodHRwOi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L3N1Yl91bnN1Yi5z aHRtbA0KDQpCZWZvcmUgcG9zdGluZywgY2hlY2sgd2FpdCB0aW1lIGF0OiBodHRwOi8vd3d3LmNj bC5uZXQNCg0KSm9iOiBodHRwOi8vd3d3LmNjbC5uZXQvam9icyANCkNvbmZlcmVuY2VzOiBodHRw Oi8vc2VydmVyLmNjbC5uZXQvY2hlbWlzdHJ5L2Fubm91bmNlbWVudHMvY29uZmVyZW5jZXMvDQoN ClNlYXJjaCBNZXNzYWdlczogaHR0cDovL3d3dy5jY2wubmV0L2h0ZGlnIChsb2dpbjogY2NsLCBQ YXNzd29yZDogc2VhcmNoKQ0KDQpJZiB5b3VyIG1haWwgYm91bmNlcyBmcm9tIENDTCB3aXRoIDUu Ny4xIGVycm9yLCBjaGVjazoNCiAgICAgIGh0dHA6Ly93d3cuY2NsLm5ldC9zcGFtbWVycy50eHQN Cg0KUlRGSTogaHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9hYm91dGNjbC9pbnN0cnVjdGlv bnMvDQo= ------=_NextPart_08041019465673444207007_002 Content-Type: text/html; charset="GB2312" Content-Transfer-Encoding: base64 PEhUTUw+PEhFQUQ+PFRJVExFPjwvVElUTEU+DQo8TUVUQSBjb250ZW50PSJLc0RIVE1MRURMaWIu b2N4LCBGcmVlV2FyZSBIVE1MIEVkaXRvciAxLjE2NC4yLCA/S3VydCBTZW5mZXIiIA0KbmFtZT1H RU5FUkFUT1I+DQo8TUVUQSBodHRwLWVxdWl2PUNvbnRlbnQtVHlwZSBjb250ZW50PSJ0ZXh0L2h0 bWw7IGNoYXJzZXQ9R0IyMzEyIj48L0hFQUQ+DQo8Qk9EWSBzdHlsZT0iRk9OVC1TSVpFOiA5cHQ7 IEZPTlQtRkFNSUxZOiDLzszlIiBsZWZ0TWFyZ2luPTUgdG9wTWFyZ2luPTUgDQojZmZmZmZmPkhp LEZsZXh4R1VJIGFuZCBNb2xlZ3JvIFZpcnR1YWwgRG9ja2VyIGlzIHF1aXRlIGZyaWVuZGx5IHdp dGggaGlnaCANCmFjY3VyYWN5Lg0KPERJVj5UaGV5IG9mZmVyIGEgcGVyaW9kIG9mIGV2YWx1YXRp b24uPC9ESVY+DQo8RElWPiZuYnNwOzwvRElWPg0KPERJVj5FbmpveSE8L0RJVj4NCjxESVY+Jm5i c3A7PC9ESVY+DQo8RElWPjwhLS1BSURfRlJPTU5BTUVfQkVHSU4tLT5BcnRodXI8IS0tQUlEX0ZS T01OQU1FX0VORC0tPiwgPEEgDQpocmVmPSJtYWlsdG86PCEtLUFJRF9GUk9NQUREUkVTU19CRUdJ Ti0tPmNvbXB1dGF0aW9uYWxib3lAZ21haWwuY29tPCEtLUFJRF9GUk9NQUREUkVTU19FTkQtLT4i PjwhLS1BSURfRlJPTUFERFJFU1NfQkVHSU4tLT5jb21wdXRhdGlvbmFsYm95QGdtYWlsLmNvbTwh LS1BSURfRlJPTUFERFJFU1NfRU5ELS0+PC9BPjwvRElWPg0KPERJVj4yMDA4LTA0LTEwIDwvRElW Pg0KPEJMT0NLUVVPVEUgDQpzdHlsZT0iUEFERElORy1SSUdIVDogMHB4OyBQQURESU5HLUxFRlQ6 IDVweDsgTUFSR0lOLUxFRlQ6IDVweDsgQk9SREVSLUxFRlQ6ICMwMDAwMDAgMnB4IHNvbGlkOyBN QVJHSU4tUklHSFQ6IDBweCI+DQogIDxESVYgDQogIHN0eWxlPSJGT05ULVdFSUdIVDogbm9ybWFs OyBGT05ULVNJWkU6IDlwdDsgTElORS1IRUlHSFQ6IG5vcm1hbDsgRk9OVC1TVFlMRTogbm9ybWFs OyBGT05ULVZBUklBTlQ6IG5vcm1hbCI+LS0tLS0gDQogIFJlY2VpdmluZyB0aGUgZm9sbG93aW5n IGNvbnRlbnQgLS0tLS0gPC9ESVY+DQogIDxESVYgDQogIHN0eWxlPSJGT05ULVdFSUdIVDogbm9y bWFsOyBGT05ULVNJWkU6IDlwdDsgQkFDS0dST1VORDogI2U0ZTRlNDsgTElORS1IRUlHSFQ6IG5v cm1hbDsgRk9OVC1TVFlMRTogbm9ybWFsOyBGT05ULVZBUklBTlQ6IG5vcm1hbDsgZm9udC1jb2xv cjogYmxhY2siPjxCPkZyb206PC9CPiANCiAgPEEgaHJlZj0ibWFpbHRvOm93bmVyLWNoZW1pc3Ry eUBjY2wubmV0Ij5IYXRpY2UgQ2FuIA0KICBhbHBoYWNhbjIwMDBfLl95YWhvby5jb208L0E+IDwv RElWPg0KICA8RElWIA0KICBzdHlsZT0iRk9OVC1XRUlHSFQ6IG5vcm1hbDsgRk9OVC1TSVpFOiA5 cHQ7IExJTkUtSEVJR0hUOiBub3JtYWw7IEZPTlQtU1RZTEU6IG5vcm1hbDsgRk9OVC1WQVJJQU5U OiBub3JtYWwiPjxCPlJlY2VpdmVyOjwvQj4gDQogIDxBIGhyZWY9Im1haWx0bzpjb21wdXRhdGlv bmFsYm95QGdtYWlsLmNvbSI+V2FuZyxKaWFuIC1pZCM0bjMtPC9BPiA8L0RJVj4NCiAgPERJViAN CiAgc3R5bGU9IkZPTlQtV0VJR0hUOiBub3JtYWw7IEZPTlQtU0laRTogOXB0OyBMSU5FLUhFSUdI VDogbm9ybWFsOyBGT05ULVNUWUxFOiBub3JtYWw7IEZPTlQtVkFSSUFOVDogbm9ybWFsIj48Qj5U aW1lOjwvQj4gDQogIDIwMDgtMDQtMTAsIDE2OjA2OjQ4PC9ESVY+DQogIDxESVYgDQogIHN0eWxl PSJGT05ULVdFSUdIVDogbm9ybWFsOyBGT05ULVNJWkU6IDlwdDsgTElORS1IRUlHSFQ6IG5vcm1h bDsgRk9OVC1TVFlMRTogbm9ybWFsOyBGT05ULVZBUklBTlQ6IG5vcm1hbCI+PEI+U3ViamVjdDo8 L0I+IA0KICBDQ0w6IHByb3RlaW4tbGlnYW5kIGRvY2tpbmcgc29mdHdhcmU8L0RJVj4NCiAgPERJ Vj48QlI+PC9ESVY+DQogIDxESVY+PC9ESVY+DQogIDxESVY+PC9ESVY+DQogIDxESVY+DQogIDxE SVY+U2VudCB0byBDQ0wgYnk6ICJIYXRpY2UgQ2FuIiBbYWxwaGFjYW4yMDAwIC4uIHlhaG9vLmNv bV08QlI+RGVhciANCiAgQWxsLDxCUj48QlI+SSB3b3VsZCBiZSB2ZXJ5IGdyYXRlZnVsIGZvciBw b2ludGVycy9hZHZpc2UgZXRjIG9uPEJSPmVzcGVjaWFsbHkgDQogIHVzZXItZnJpZW5kbHkgc29m dHdhcmUgYW5kIHJldmlld3MvbGl0ZXJhdHVyZSBzdWl0YWJsZSBmb3IgYTxCUj5uZXdjb21lciB0 byANCiAgbW9sZWN1bGFyIGRvY2tpbmcgKHByb3RlaW4vcHJvdGVpbi8sIHByb3RlaW4vbGlnYW5k KS48QlI+PEJSPk1hbnkgdGhhbmtzIGFuZCANCiAga2luZCByZWdhcmRzPEJSPjxCUj5IYXRpY2U8 QlI+PEJSPjxCUj48QlI+LT0gVGhpcyBpcyBhdXRvbWF0aWNhbGx5IGFkZGVkIHRvIA0KICBlYWNo IG1lc3NhZ2UgYnkgdGhlIG1haWxpbmcgc2NyaXB0ID0tPEJSPlRvIHJlY292ZXIgdGhlIGVtYWls IGFkZHJlc3Mgb2YgdGhlIA0KICBhdXRob3Igb2YgdGhlIG1lc3NhZ2UsIHBsZWFzZSBjaGFuZ2U8 QlI+dGhlIHN0cmFuZ2UgY2hhcmFjdGVycyBvbiB0aGUgdG9wIGxpbmUgDQogIHRvIHRoZSBAIHNp Z24uIFlvdSBjYW4gYWxzbzxCUj5sb29rIHVwIHRoZSBYLU9yaWdpbmFsLUZyb206IGxpbmUgaW4g dGhlIG1haWwgDQogIGhlYWRlci48QlI+PEJSPkUtbWFpbCB0byBzdWJzY3JpYmVyczogPEEgDQog IGhyZWY9Im1haWx0bzogQ0hFTUlTVFJZQGNjbC5uZXQiPkNIRU1JU1RSWUBjY2wubmV0PC9BPiBv ciANCiAgdXNlOjxCUj4mbmJzcDsmbmJzcDsmbmJzcDsmbmJzcDsmbmJzcDsmbmJzcDs8QSANCiAg aHJlZj0iaHR0cDovL3d3dy5jY2wubmV0L2NnaS1iaW4vY2NsL3NlbmRfY2NsX21lc3NhZ2UiPmh0 dHA6Ly93d3cuY2NsLm5ldC9jZ2ktYmluL2NjbC9zZW5kX2NjbF9tZXNzYWdlPC9BPjxCUj48QlI+ RS1tYWlsIA0KICB0byBhZG1pbmlzdHJhdG9yczogPEEgDQogIGhyZWY9Im1haWx0bzogQ0hFTUlT VFJZLVJFUVVFU1RAY2NsLm5ldCI+Q0hFTUlTVFJZLVJFUVVFU1RAY2NsLm5ldDwvQT4gb3IgDQog IHVzZTxCUj4mbmJzcDsmbmJzcDsmbmJzcDsmbmJzcDsmbmJzcDsmbmJzcDs8QSANCiAgaHJlZj0i aHR0cDovL3d3dy5jY2wubmV0L2NnaS1iaW4vY2NsL3NlbmRfY2NsX21lc3NhZ2UiPmh0dHA6Ly93 d3cuY2NsLm5ldC9jZ2ktYmluL2NjbC9zZW5kX2NjbF9tZXNzYWdlPC9BPjxCUj48QlI+U3Vic2Ny aWJlL1Vuc3Vic2NyaWJlOiANCiAgPEJSPiZuYnNwOyZuYnNwOyZuYnNwOyZuYnNwOyZuYnNwOyZu YnNwOzxBIA0KICBocmVmPSJodHRwOi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L3N1Yl91bnN1Yi5z aHRtbCI+aHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9zdWJfdW5zdWIuc2h0bWw8L0E+PEJS PjxCUj5CZWZvcmUgDQogIHBvc3RpbmcsIGNoZWNrIHdhaXQgdGltZSBhdDogPEEgDQogIGhyZWY9 Imh0dHA6Ly93d3cuY2NsLm5ldCI+aHR0cDovL3d3dy5jY2wubmV0PC9BPjxCUj48QlI+Sm9iOiA8 QSANCiAgaHJlZj0iaHR0cDovL3d3dy5jY2wubmV0L2pvYnMiPmh0dHA6Ly93d3cuY2NsLm5ldC9q b2JzPC9BPiA8QlI+Q29uZmVyZW5jZXM6IDxBIA0KICBocmVmPSJodHRwOi8vc2VydmVyLmNjbC5u ZXQvY2hlbWlzdHJ5L2Fubm91bmNlbWVudHMvY29uZmVyZW5jZXMvIj5odHRwOi8vc2VydmVyLmNj bC5uZXQvY2hlbWlzdHJ5L2Fubm91bmNlbWVudHMvY29uZmVyZW5jZXMvPC9BPjxCUj48QlI+U2Vh cmNoIA0KICBNZXNzYWdlczogPEEgaHJlZj0iaHR0cDovL3d3dy5jY2wubmV0L2h0ZGlnIj5odHRw Oi8vd3d3LmNjbC5uZXQvaHRkaWc8L0E+IA0KICAobG9naW46IGNjbCwgUGFzc3dvcmQ6IHNlYXJj aCk8QlI+PEJSPklmIHlvdXIgbWFpbCBib3VuY2VzIGZyb20gQ0NMIHdpdGggNS43LjEgDQogIGVy cm9yLCBjaGVjazo8QlI+Jm5ic3A7Jm5ic3A7Jm5ic3A7Jm5ic3A7Jm5ic3A7Jm5ic3A7PEEgDQog IGhyZWY9Imh0dHA6Ly93d3cuY2NsLm5ldC9zcGFtbWVycy50eHQiPmh0dHA6Ly93d3cuY2NsLm5l dC9zcGFtbWVycy50eHQ8L0E+PEJSPjxCUj5SVEZJOiANCiAgPEEgDQogIGhyZWY9Imh0dHA6Ly93 d3cuY2NsLm5ldC9jaGVtaXN0cnkvYWJvdXRjY2wvaW5zdHJ1Y3Rpb25zLyI+aHR0cDovL3d3dy5j Y2wubmV0L2NoZW1pc3RyeS9hYm91dGNjbC9pbnN0cnVjdGlvbnMvPC9BPjxCUj48QlI+PEJSPjwv RElWPjwvRElWPjwvQkxPQ0tRVU9URT48L0JPRFk+PC9IVE1MPg0K ------=_NextPart_08041019465673444207007_002-- From owner-chemistry@ccl.net Fri Apr 11 03:20:00 2008 From: "Raji Raji raji#anal.chem.tohoku.ac.jp" To: CCL Subject: CCL: Atom fixing or freezing Message-Id: <-36699-080411031901-4417-WAblihHHRp0J61iRYD+s6w{=}server.ccl.net> X-Original-From: "Raji Raji" Date: Fri, 11 Apr 2008 03:18:56 -0400 Sent to CCL by: "Raji Raji" [raji[#]anal.chem.tohoku.ac.jp] Dear Durairajan, The keyword "modredundant" is useful to freeze the redundant internal coordinates. Say for example, if u want to freeze the distance between two atoms... atom 1 and 18, and lets say if the distance between them is 2.77 angstrom then after the coordinates leave a blank line then type 1 18 2.77 F Likewise you can specify for angle and dihedral angle. Dont forget to leave another blank line at the end of the input. Hope it helps. With Kind Regards, Raji. From owner-chemistry@ccl.net Fri Apr 11 03:58:00 2008 From: "Hemant Srivastava hemantkrsri*o*gmail.com" To: CCL Subject: CCL:G: Atom fixing or freezing Message-Id: <-36700-080410165910-20831-fgaNHYM2UYdNWeiEK69HVQ-,-server.ccl.net> X-Original-From: "Hemant Srivastava" Content-Type: multipart/alternative; boundary="----=_Part_17202_7292664.1207857634408" Date: Thu, 10 Apr 2008 23:00:34 +0300 MIME-Version: 1.0 Sent to CCL by: "Hemant Srivastava" [hemantkrsri{:}gmail.com] ------=_Part_17202_7292664.1207857634408 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, For fixing the atoms in optimization, you can just write at bottom line, X 1 F X 18 F where 1 and 18 are the atom numbers. So you are missing to write just X Hope it will help Good luck Regards, Hemant The Hebrew University of Jerusalem ============================== On Thu, Apr 10, 2008 at 9:30 PM, Durairajan Senthilnathan zenthil03a/ yahoo.co.in wrote: > > Sent to CCL by: "Durairajan Senthilnathan" [zenthil03:+:yahoo.co.in] > Dear CCL'rs > Greetings. I want to fix( or freeze) a atom in a 3D space for > gaussian calculation. I want to keep this atom as without movement when > optimaization and transition state calculation. > > my input file is > > %chk=model.chk > %mem=6MW > %nproc=1 > #p opt=modredundant freq am1 > > Title Card Required > > 0 1 > C -1.04910715 -0.35714285 0.00000000 > H -0.69243431 0.14725534 0.87365150 > H -0.69243431 0.14725534 -0.87365150 > H -2.11910715 -0.35712967 0.00000000 > C -0.53579143 -1.80907500 0.00000000 > H -0.89246389 -2.31347306 0.87365174 > H -0.89246472 -2.31347389 -0.87365092 > C 1.00420857 -1.80909321 -0.00000123 > H 1.36088018 -1.30469693 -0.87365435 > H 1.36088208 -1.30469210 0.87364831 > C 1.51752428 -3.26102536 0.00000272 > H 1.16085397 -3.76542151 0.87365644 > H 1.16085150 -3.76542742 -0.87364657 > H 2.58752428 -3.26103580 0.00000120 > H 2.53166275 -0.48629618 0.52184131 > C 2.17500833 0.52251382 0.52184131 > H 2.53168117 1.02691201 1.39549281 > H 1.10500833 0.52252701 0.52184131 > C 2.68835054 1.24847009 -0.73556366 > H 2.33009962 2.25671377 -0.73654241 > H 3.75834878 1.25015115 -0.73458588 > H 2.33327591 0.74294331 -1.60921386 > > 1 F > 18 F > > Here I want to fix or freez atoms 1 and 18. > I have error at filanally as error in output finalising step. > > How can I avoid this error? any one of you give me a better solution for > my error. > > best wishes from > Bharathidasan University> > > ------=_Part_17202_7292664.1207857634408 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi,
 
For fixing the atoms in optimization, you can just write at bottom line,
 
X 1 F
X 18 F
 
where 1 and 18 are the atom numbers.
 
 
So you are missing to write just X
 
Hope it will help
 
Good luck
 
Regards,
Hemant
The Hebrew University of Jerusalem
==============================

On Thu, Apr 10, 2008 at 9:30 PM, Durairajan Senthilnathan zenthil03a/yahoo.co.in <owner-chemistry()ccl.net> wrote:

Sent to CCL by: "Durairajan  Senthilnathan" [zenthil03:+:yahoo.co.in]
Dear CCL'rs
         Greetings. I want to fix( or freeze) a atom in a 3D space for gaussian calculation. I want to keep this atom as without movement when optimaization and transition state calculation.

my input file is

%chk=model.chk
%mem=6MW
%nproc=1
#p opt=modredundant freq am1

Title Card Required

0 1
 C                 -1.04910715   -0.35714285    0.00000000
 H                 -0.69243431    0.14725534    0.87365150
 H                 -0.69243431    0.14725534   -0.87365150
 H                 -2.11910715   -0.35712967    0.00000000
 C                 -0.53579143   -1.80907500    0.00000000
 H                 -0.89246389   -2.31347306    0.87365174
 H                 -0.89246472   -2.31347389   -0.87365092
 C                  1.00420857   -1.80909321   -0.00000123
 H                  1.36088018   -1.30469693   -0.87365435
 H                  1.36088208   -1.30469210    0.87364831
 C                  1.51752428   -3.26102536    0.00000272
 H                  1.16085397   -3.76542151    0.87365644
 H                  1.16085150   -3.76542742   -0.87364657
 H                  2.58752428   -3.26103580    0.00000120
 H                  2.53166275   -0.48629618    0.52184131
 C                  2.17500833    0.52251382    0.52184131
 H                  2.53168117    1.02691201    1.39549281
 H                  1.10500833    0.52252701    0.52184131
 C                  2.68835054    1.24847009   -0.73556366
 H                  2.33009962    2.25671377   -0.73654241
 H                  3.75834878    1.25015115   -0.73458588
 H                  2.33327591    0.74294331   -1.60921386

 1 F
 18 F

Here I want to fix or freez atoms 1 and 18.
I have error at filanally as error in output finalising step.

How can I avoid this error? any one of you give me a better solution for my error.

best wishes from
Bharathidasan University



E-mail to subscribers: CHEMISTRY()ccl.net or use:
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST()ccl.net or use
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
     http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

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

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



------=_Part_17202_7292664.1207857634408-- From owner-chemistry@ccl.net Fri Apr 11 05:50:01 2008 From: "Pascal Boulet pascal.boulet|,|univ-provence.fr" To: CCL Subject: CCL: ab initio calculation for Fe3+ complex Message-Id: <-36701-080411043730-18076-CppTkjxVkPjXbJ0+0eMTIg^^^server.ccl.net> X-Original-From: Pascal Boulet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 11 Apr 2008 10:39:43 +0200 MIME-Version: 1.0 Sent to CCL by: Pascal Boulet [pascal.boulet:univ-provence.fr] Dear Lily, Chunhui Li baotogo2004*gmail.com wrote: > Sent to CCL by: "Chunhui Li" [baotogo2004,gmail.com] > Dear All, > > I need to do an ab initio calculation on a Fe complex. The complex is Fe3+ (H2O)5 with an fluorocarbon which has an COO- end. The total size is about 30-40 atoms. I am using Spartan '06 window to find equilibrium geometry. > > my first question is to verify that my total charge is +2 and multiplicity is 6, is it right? Since the Fe3+ charge I got from optimization using UHF STO3G is 2.05, not 3, I am confused with the coordination chemistry on Fe3+. > There is of course a difference between formal charges (+3) and charges calculated using ab initio methods (+2.05). Roughly speaking, the difference between formal charges and ab initio charges reflects the difference between a totally ionic complex and the "true" complex. The formal charge for your molecule is +2, assuming that the formal charge on iron is +3. The fact that you obtain a +2.05 ab initio charge on Fe looks correct, although I would have expected an even lower charge (+1.6-1.8)! But I suppose this is a Mulliken charge, and Mulliken scheme tends to give too ionic charges. In addition, the basis set you use is far too small which prevents flexibility for a larger delocalisation of the electrons. Now for the multiplicity, if you are not sure, you should make "experiments" with various, appropriate mulitiplicities. > my second question is: what method and basis set you think would be appropriate for this system? Will HF method work for just geometry optimization? I tried to use UHF 3-21G to optimize, but SCF failed to converge after 500 cycles. STO-3G did converge. > In this case HF is a starting point for a calculation of better quality. You will need correlation energy for such a system, which is not accounted for in the HF method. If you cannot afford MP2 calculations, I would suggest a GGA-DFT method which is about the same computational effort as HF. > My computer have 512M memory, do you think I need more memory for this calculation? > See next answer on how to reduce the memory and reaching "better" quality. > another question is that I don't understand why 6-311G* and 6-311+G** don't work for this system. The output says Basis not supported for the above atom.( I assume it is not working for Fe, isn't it?) > Yes, probably. I don't know spartan, but is it possible to use "Effective Core Potentials" for core electrons? You would save time and memory, and you would get reliable results in combination with MP2 or DFT-GGA calculations. > My last question is: which one is better, UHF or ROHF in this case? > It really depends on what you are interested in! If you just want an optimized structure, I would start with ROHF first to same time (and eventually restart this calculation with UHF option to make sure you have a "good" geometry). But if you are interested in spin densities partition, of course, UHF calculation is compulsory. > Thank you in advance! > I hope this help. Pascal > Lily> > > -- Dr. Pascal Boulet, Computational Chemist University of Provence Laboratoire Chimie Provence, UMR6264 Centre Saint-Jerome, case MADIREL F-13397 MARSEILLE Cedex 20, France Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11 courriel: pascal.boulet_+_univ-provence.fr http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet From owner-chemistry@ccl.net Fri Apr 11 05:53:01 2008 From: "Mariusz Radon mariusz.radon-#-gmail.com" To: CCL Subject: CCL: ab initio calculation for Fe3+ complex Message-Id: <-36702-080411053500-3357-hnR6G9kgjLoPyytDwVW8Og:server.ccl.net> X-Original-From: Mariusz Radon Content-Type: text/plain; charset=us-ascii Date: Fri, 11 Apr 2008 11:34:22 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon-#-gmail.com] Dear Chunhui: > my first question is to verify that my total charge is +2 and > multiplicity is 6, is it right? As to multiplicity: for transition metal complexes you often cannot assign it in advance. In general, you should compare several cases. There is plenty of papers in this topic, see e.g. the names of Harvey and Pierloot. But for your case I would also expect the sextet to be the ground state. > Since the Fe3+ charge I got from optimization using UHF STO3G > is 2.05, not 3, I am confused with the coordination chemistry on Fe3+. If you are using Mulliken or similar population analysis don't expect to reproduce the formal oxidation state (+3). However, look at the spin population of iron: it should be close to 5 unpaired electrons. > my second question is: what method and basis set you think would be > appropriate for this system? Will HF method work for just geometry > optimization? I tried to use UHF 3-21G to optimize, but SCF failed to > converge after 500 cycles. STO-3G did converge. STO-3G is definitely too small for iron for almost any quantitative considerations. I think you must use larger basis. > My last question is: which one is better, UHF or ROHF in this case? I think you should definitely use DFT, not HF for transition metal system! The question of appropriate functional is of course perrenial. But there is still the dillema whether to choose Resticted Open-Shell (RO-) or Unresticted (U-) version. As far as I know the majority of papers from transistion metal chemistry employ U-DFT formalism and it is sometimes claimed to work better, but I don't remember any paper systematically comparing both approaches. best regards, Mariusz Radon From owner-chemistry@ccl.net Fri Apr 11 06:28:00 2008 From: "Maxim Kholin maxim.kholin**q-pharm.com" To: CCL Subject: CCL: protein-ligand docking software Message-Id: <-36703-080411034032-13643-OBnt2Fw7uvPLE7KS5Zua5Q-x-server.ccl.net> X-Original-From: "Maxim Kholin" Content-Type: multipart/alternative; boundary="----=_NextPart_000_028B_01C89BC9.1544A090" Date: Fri, 11 Apr 2008 11:42:12 +0400 MIME-Version: 1.0 Sent to CCL by: "Maxim Kholin" [maxim.kholin * q-pharm.com] This is a multi-part message in MIME format. ------=_NextPart_000_028B_01C89BC9.1544A090 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: quoted-printable Hi,=20 There is an option to use pure physics based docking and IC50 = calculation tool Quantum for free at www.leadfinding.com working with = ChemDiv diversified library.=20 Maxim ------=_NextPart_000_028B_01C89BC9.1544A090 Content-Type: text/html; charset="GB2312" Content-Transfer-Encoding: quoted-printable
Hi,
There is an option to use pure physics = based=20 docking and IC50 calculation tool Quantum for free at www.leadfinding.com working with = ChemDiv=20 diversified library.
 
Maxim
 
------=_NextPart_000_028B_01C89BC9.1544A090-- From owner-chemistry@ccl.net Fri Apr 11 07:42:01 2008 From: "Mikael Johansson mpjohans%x%chem.au.dk" To: CCL Subject: CCL: ab initio calculation for Fe3+ complex Message-Id: <-36704-080411074117-17032-rpfo0i6oGUDjiletMQWm9A.@.server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 11 Apr 2008 13:41:05 +0200 MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mpjohans^^^chem.au.dk] Hello Lily and All! > Chunhui Li baotogo2004*gmail.com wrote: >> I need to do an ab initio calculation on a Fe complex. The complex is Fe3+ >> (H2O)5 with an fluorocarbon which has an COO- end. Just adding a bit to the quite complete answers by Pascal and Mariusz. I fully agree that DFT is the method of choice here, although it will have problems in conclusively deciding the correct spin state. It will probably give better results than MP2, too. B3LYP has of course been used extensively, but perhaps an even better choice would be BP86. It's non-hybrid, so depending on your program it can speed up calculations significantly. It might even get you a better geometry than B3LYP, see: Ryde and Nilsson, Quantum chemistry can locally improve protein crystal structures", JACS 125 (2003) 14232. Also, use UHF instead of ROHF. TM systems exhibit a lot of spin polarisation, which a restricted formalism naturally cannot capture. I'm not aware of a DFT ROKS comparison, but for nice colour pictures on the complete failure of Hartree-Fock at both UHF and ROHF levels for another iron complex (haem), I modestly suggest page 40 of my thesis: http://www.iki.fi/~mpjohans/science/thesis-summary-2007.pdf And yes, using ridiculously small basis sets will give you results of equal hilarity. Have a good weekend, Mikael J. http://www.iki.fi/~mpjohans From owner-chemistry@ccl.net Fri Apr 11 08:28:00 2008 From: "Gijs Schaftenaar schaft###cmbi.ru.nl" To: CCL Subject: CCL: International Drug Discovery Course 2008 Message-Id: <-36705-080411082652-7931-FDAHXLtQDd1FvdKyLJQ18A:_:server.ccl.net> X-Original-From: "Gijs Schaftenaar" Date: Fri, 11 Apr 2008 08:26:49 -0400 Sent to CCL by: "Gijs Schaftenaar" [schaft ~~ cmbi.ru.nl] > From June 23 - July 4 2008, the Computational Drug Discovery Group of the Centre of Molecular and Biomolecular Informatics (CMBI) will present the sixth "Computational Drug Discovery Course". The course will be held at the Radboud University of Nijmegen in the Netherlands. This course was developed together with the pharmaceutical company Organon. The two-week course describes some of the recent advances in drug discovery informatics, with a focus on the application of e-science to real life problems. The course is targeted at MSc and PhD students, and postdocs, who are interested in the field of computational target and drug discovery. The fee for the course is 100 euro. The course is financially supported by the dutch funding agency NBIC. Tripos supports the course with educational licenses for their Sybyl software. For more information see the course website (http://www.cmbi.ru.nl/ICDD2008/) or the flyer (http://www.cmbi.ru.nl/edu/bioinf4/ICDD2008.pdf) Sincerely Yours, Dr. Gijs Schaftenaar Dr. Sander Nabuurs Prof. Jacob de Vlieg From owner-chemistry@ccl.net Fri Apr 11 09:03:01 2008 From: "Uwe Huniar uwe.huniar:-:cosmologic.de" To: CCL Subject: CCL: Parameters nppa, nspa, disex, rsolv = min(rad(h)), routf in Turbomole Message-Id: <-36706-080411083908-16309-zZlk6rggq8dixYUQZRMiQg*|*server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 11 Apr 2008 14:39:28 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar-.-cosmologic.de] Hello, we should not continue the discussion in the CCL, I think this is too much a technical issue to be of general interest. I am not sure how you compare TDDFT results with experiment. Would you mind sending the coordinates, the input file (control), calculated and experimental spectra to the Turbomole Support? We could check the input for possible pitfalls and give you some hints about the COSMO settings in Turbomole. Regards, Uwe > Dear Michael and other Colleagues, > > Thank you for giving values of epsilon = 78.5 for water and epsilon = > 32.6 for methanol in Turbomole. > > Would you please to say do are good for both water and methanol > the default Turbomole values: > > nppa = 10082 > nspa = 92 > disex = 10.0 > rsolv = min(rad(h)) routf = 0.85 when calculating the TD DFT B3LYP? > Maybe my bad obtained spectrum calculating by Turbomole is due to not > right default values > of these parameters installed in Turbomole? > > I did not found the meaning, description and tabulation the parameters > nppa, > nspa, disex, rsolv = min(rad(h)), routf for water and methanol in the > Turbomole_Tutorial_59.pdf and Turbomole DOK.pdf. > > Maybe somebody have experience in using TD DFT by COSMO with Turbomole > and can send me papers describing the values of nppa, nspa, disex, rsolv > = min(rad(h)), routf for both water and methanol? > > With best regards, > Arvydas Tamulis > > On Tue, 8 Apr 2008, TURBOMOLE SUPPORT wrote: > >> >>> What are the epsilon values for water and methanol molecules in cosmo >>> Turbomole? >> You can specify it it in the control file like: >> $cosmo >> ... >> epsilon = 78.5 >> ... >> >> Or give it in the first dialog of cosmoprep >> The value for water is 78.5, the one for methanol 32.6, You can find >> mor constsnts in the "Handbook of Chemistry an Physicas " and many >> other sources. >> As Uwe already wrote >>>> >>>> COSMO is not fully implemented in the TDDFT part of Turbomole in the >>>> official release. The so called 'fast term' in the CPKS equations is >>>> missing. The developers version of Turbomole has a full >>>> implementation which will be included in the next version - but as >>>> far as I know, this term has only small contributions to the excited >>>> state energies. >> So, you can calc. spectra by taking into account the solvent effctes >> of the ground state only. >> >> Best regards, >> >> The TURBOMOLE Team (Michael) >> > > -- ------------------------------------------------------------------------------ Dr. Uwe Huniar COSMOlogic GmbH&Co.KG Burscheider Str. 515 D-51381 Leverkusen Germany Tel. +49 - 2171 - 36 36 65 Fax +49 - 2171 - 73 16 89 EMail: uwe.huniar()cosmologic.de turbomole()cosmologic.de info()turbomole.com From owner-chemistry@ccl.net Fri Apr 11 09:48:01 2008 From: "Guanna Li gnli,,dicp.ac.cn" To: CCL Subject: CCL: theory relate to circular dichroism sepctrum (ECD) Message-Id: <-36707-080411025254-1324-CFZb8NSgysV8KSsEUi7gNw]=[server.ccl.net> X-Original-From: "Guanna Li" Content-Transfer-Encoding: base64 Content-Type: text/plain; charset="gb2312" Date: Fri, 11 Apr 2008 14:51:48 +0800 Mime-Version: 1.0 Sent to CCL by: "Guanna Li" [gnli]![dicp.ac.cn] RGVhciAgQ0NMZXIsDQpJIGdvdCBteSBmaXJzdCBzZW1pbmFyIHRpdGxlIDogdGhlb3J5IGFuZCBl eHBlcmltZW50IG9mIGNpcmN1bGFyIGRpY2hyb2lzbSBzcGVjdHJ1bSAoQ0Qpo6xJIGRvd25sb2Fk IHNvbWUgYXJ0aWNsZXMgYnV0IG1vc3Qgb2YgdGhlbSBpcyBhYm91dCBleHBlcmltZW50YWwgYW5k IGRmdCBjYWxjdWxhdGUgcmVzdWx0Lg0KdGhleSBhcmUgaGFyZGx5IHJlZmVyIHRvIHRoZSBiYXNp YyB0aGVvcnkgb2YgQ0QgaW4gdGhlIGludHJvZHVjdGlvbiBvciB0aGVvcnkgcGFydC4NCkkgd2ls bCB2ZXJ5IGFwcHJlY2lhdGUgaWYgYW55b25lIGNhbiByZWNvbW1lbmQgc29tZSBwYXBlciBhYm91 dCB0aGUgdGhlb3J5IG9mIENEIGZvciBtZS4NClRoYW5rIHlvdSAhIA0KIAkJCQkNCkJlc3Qgd2lz aGVzIA0KR3Vhbm5hIExpDQo= From owner-chemistry@ccl.net Fri Apr 11 10:13:01 2008 From: "Stephanie Gulde sgulde,ipb-halle.de" To: CCL Subject: CCL: converting a text file with systematic names into structure files Message-Id: <-36708-080411030000-2599-20ZFsZ8JWxBspU+TVmxpGA ~ server.ccl.net> X-Original-From: "Stephanie Gulde" Date: Fri, 11 Apr 2008 02:59:56 -0400 Sent to CCL by: "Stephanie Gulde" [sgulde[*]ipb-halle.de] Hallo, does somebody know a program which converts a text file with systematic names into structure files? Thank you! Yours sincerely Stephanie From owner-chemistry@ccl.net Fri Apr 11 10:48:00 2008 From: "Richard Leo Wood woodx278.[a].umn.edu" To: CCL Subject: CCL: Problem in finding Charge and Spin Multiplicity Message-Id: <-36709-080411104632-13815-vUdw6sPzBMXnB/hh0rJP5Q[a]server.ccl.net> X-Original-From: "Richard Leo Wood" Date: Fri, 11 Apr 2008 10:46:28 -0400 Sent to CCL by: "Richard Leo Wood" [woodx278||umn.edu] Hi all, I had a similar problem last week. I had a system that I had removed a proton from and so it had a charge of -1. However, since it still had the same number of atoms, it was still a singlet, even though I tried to call it a doublet. Perhaps that is the problem here? BTW, it was good to see some of you at the ACS meeting and put names and faces together. Richard Sent to CCL by: "Close, David M." [CLOSED * mail.etsu.edu] This is easy. The multiplicity is related to an open shell system. You must either have an oxidized molecule (one electron removed) or a reduced molecule (one electron addeded). In either case the multiciplicity is 2I+1. For an electron the nuclear spin is 1/2, so 2I+1 = 2. But the program is confused because when it counts the number of electrons (in your case 66) this is an even number. Therefore you do not have an open-shell. Look at your input. You must have left off a proton or something trivial like that. From owner-chemistry@ccl.net Fri Apr 11 11:29:01 2008 From: "Frank Neese neese(0)thch.uni-bonn.de" To: CCL Subject: CCL: Spin state question Message-Id: <-36710-080411104458-13115-wWkWeZORACMkKWilqg8T0g---server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 11 Apr 2008 15:44:38 +0200 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese~!~thch.uni-bonn.de] Dear ladies and gentlemen, since there has been so much discussion on the spin state of the complex: Fe3+ (H2O)5 with an fluorocarbon which has an COO- end My opinion: in this case there is only one chemically reasonable suggestion: high-spin Fe(III), S=5/2. H2O is a weak field ligand and carboxylate is as well. If any DFT predicts a low spin state that would with high probability be wrong, but i doubt that this would be the case. The spin state is also easily checked experimentally. Best regards, Frank -- --------------------------------------------------------------- Prof. Dr. Frank Neese Lehrstuhl fuer Theoretische Chemie Universitaet Bonn Wegelerstr. 12 D-53115 Bonn, Germany neese-x-thch.uni-bonn.de Phone: +49-28-732351 FAX: +49-(0)228-739064 --------------------------------------------------------------- From owner-chemistry@ccl.net Fri Apr 11 11:57:01 2008 From: "Miguel Gonzalez miguel.gonzalez[#]ub.edu" To: CCL Subject: CCL: projected vs. unprojected MPn benchmarks? Message-Id: <-36711-080411101032-15450-Sn8pi/0nunbLS8NzEJnLuQ^server.ccl.net> X-Original-From: Miguel Gonzalez Content-transfer-encoding: QUOTED-PRINTABLE Content-type: text/plain; reply-type=original; charset=iso-8859-1; format=flowed Date: Fri, 11 Apr 2008 15:38:08 +0200 MIME-version: 1.0 Sent to CCL by: Miguel Gonzalez [miguel.gonzalez**ub.edu] 11 April 2008 Hi Mariusz, A comparison between MPn and PMPn methods can be found in this paper = on=20 chemical laser systems: R. Say=F3s, J. Hernando, J. Hijazo y M. Gonz=E1lez An analytical potential energy surface of the HClF(2A') system based = on ab=20 initio calculations. Variational transition state theory study of the= H +=20 ClF =AE F + HCl, Cl + HF and F + HCl =AE Cl + HF reactions and their = deuterium=20 isotope variants Physical Chemistry Chemical Physics, 1, 947-956 (1999) I hope this could be helpful, Miguel Gonzalez PS. By the way, perhaps some useful practical ideas on the interest of us= ing the=20 PMPn//MPn approach given in the following papers on gas phase reactio= ns of=20 interest in atmospheric chemistry and combustion processes could also= be of=20 interest for you: M. Gonz=E1lez et al. Ab initio ground potential energy surface, VTST = and QCT=20 study of the O(3P) + CH4(X1A1) =AE OH(X2P) + CH3(X2A2") reaction. Jou= rnal of=20 Chemical Physics, 110, 7326-7338 (1999) M. Gonz=E1lez et al. Ab initio ground potential energy surface and= =20 quasiclassical trajectory study of the O(1D) + CH4(X1A1) =AE OH(X2P) = +=20 CH3(X2A2") reaction dynamics. Journal of Chemical Physics, 111, 8913-= 8924=20 (1999) R. Say=F3s et al. A theoretical approach to the O(1D) + H2O(X1A1) rea= ction: Ab=20 initio potential energy surface and quasiclassical trajectory dynamic= s=20 study. Journal of Chemical Physics, 113, 6736-6747 ( 2000) D. Troya et al. Ab initio, kinetics and dynamics study of Cl + CH4 = =AE HCl +=20 CH3. Journal of Chemical Physics, 117, 5730-5741 (2002) D. Troya et al. Ab initio potential energy surface, variational trans= ition=20 state theory, and quasiclassical trajectory studies of the F + CH4 = =AE HF +=20 CH3 reaction. Journal of Chemical Physics,120, 5181-5191 (2004) ----- Original Message -----=20 =46rom: "Mariusz Radon mariusz.radon/agmail.com" To: "Gonzalez, Miguel " Sent: Wednesday, April 09, 2008 3:45 PM Subject: CCL: projected vs. unprojected MPn benchmarks? > > Sent to CCL by: Mariusz Radon [mariusz.radon-*-gmail.com] > Dear David and Lukasz: > > Thank you very much for your answers and useful references! > > However, if anyone could provide me more reference on > UMPn vs. PMPn benchmarks I would be very thankful. > > best regards, > Mariusz Radon > > --=20 > Mariusz Radon > Department of Theoretical Chemistry > Jagiellonian University > mradon /at/ chemia.uj.edu.pl > http://www.chemia.uj.edu.pl/~mradon > > > > -=3D This is automatically added to each message by the mailing scr= ipt =3D- > To recover the email address of the author of the message, please c= hange> Conferences: http://server.ccl.net/chemistry/announcements/conferen= ces/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: s= earch)> > >=20 From owner-chemistry@ccl.net Fri Apr 11 12:42:00 2008 From: "Greg Warren greg\a/eyesopen.com" To: CCL Subject: CCL: converting a text file with systematic names into structure files Message-Id: <-36712-080411121606-22393-2Qergr/O4i9bYJNCuk4H3w=-=server.ccl.net> X-Original-From: Greg Warren Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 11 Apr 2008 09:14:28 -0600 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg(-)eyesopen.com] Dear Stephanie, OpenEye Software Inc. has a application and programming toolkit to do this. The product is called Lexichem and the application is nam2mol. It is free of charge to academics http://www.eyesopen.com/forms/academic_license_app.php. If you are a commercial user then a two month evaluation license is available as well at http://www.eyesopen.com/forms/eval_request.php. Regards, Greg -- ======================================== Gregory Warren, PhD OpenEye Scientific Software, Inc 9 Bisbee Court, Suite D Santa Fe, NM 87508 (505) 473-7385 ext 50 mailto:greg|a|eyesopen.com ======================================== Stephanie Gulde sgulde,ipb-halle.de wrote: > Sent to CCL by: "Stephanie Gulde" [sgulde[*]ipb-halle.de] > Hallo, > does somebody know a program which converts a text file with systematic names into structure files? > > Thank you! > > Yours sincerely > Stephanie> > > From owner-chemistry@ccl.net Fri Apr 11 13:15:01 2008 From: "Ashish Datt ashish_cares]^[hotmail.com" To: CCL Subject: CCL:G: Zeolite Modelling Message-Id: <-36713-080411130941-26033-8pF/qKXZfvpkajLefYGJIg:_:server.ccl.net> X-Original-From: "Ashish Datt" Date: Fri, 11 Apr 2008 13:09:37 -0400 Sent to CCL by: "Ashish Datt" [ashish_cares~!~hotmail.com] Well I wish to model zeolites through quantum mechanical softwares so I would like to ask for which is the best software to do that Eg Gaussian or Gamess or something else and also some tips to do that as I am pretty new in this field. thanks Ashish From owner-chemistry@ccl.net Fri Apr 11 13:56:00 2008 From: "Imran Predhanekar imranpkm++gmail.com" To: CCL Subject: CCL: Freezing & Optimisation Message-Id: <-36714-080411133848-16421-vLQuCHF8xaZaTJwRdw4zCQ() server.ccl.net> X-Original-From: "Imran Predhanekar" Date: Fri, 11 Apr 2008 13:38:44 -0400 Sent to CCL by: "Imran Predhanekar" [imranpkm\a/gmail.com] Hello, I did full optimisation of an amino acid (24 atoms) at B3LYP 6-311(dp) for which it took about 90 minutes. In order to find out the charge release into the residue upon substitution, I Froze all the other atoms (residue) and optimized only the R group (-CH3) using IFREEZ(1) for about 60 coordinates (20 atoms). The time it took for partial optimisation was about 340 minutes (4 atoms!). Is it expected given the fact that a partial optimisation involves only a few atoms? I would be thankful for any explanation. Regards Imran Predhanekar From owner-chemistry@ccl.net Fri Apr 11 16:01:01 2008 From: "Denis J Gulin deninho%a%quimica.ufpr.br" To: CCL Subject: CCL: calculations of NMR parameters Message-Id: <-36715-080411145622-30676-ni9WRYepUmChYWfkLaqFHw^^server.ccl.net> X-Original-From: "Denis J Gulin" Date: Fri, 11 Apr 2008 14:56:17 -0400 Sent to CCL by: "Denis J Gulin" [deninho[*]quimica.ufpr.br] Hi, Could anyone suggest me a reference about "the validity" for results of NMR parameters calculations at a certain level of theory (or theory model) based on optimized geometries obtained at another level, p.e., magnetic shieldings calculated at B3LYP/6-31g(d,p)//MP2/6-311++G(d,p). Thanks in advance, ===== Denis From owner-chemistry@ccl.net Fri Apr 11 16:35:01 2008 From: "David Gallagher gallagher.da]![gmail.com" To: CCL Subject: CCL:G: Zeolite Modelling Message-Id: <-36716-080411155405-5851-tNhtP8lFy+gZ2nGWmXSn7g_+_server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_16415140==.ALT" Date: Fri, 11 Apr 2008 11:17:55 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da(-)gmail.com] --=====================_16415140==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Ashish, Depending on the size of the zeolite, if you find it is too large or too slow for ab initio methods, you should try semi-empirical. The new PM6 method in MOPAC2007 works well for crystals and uses 'translation vectors' to deal with extended solids (and it's free for academics: http://www.cacheresearch.com/mopac.html ). There are some example of zeolites structures optimized with MOPAC2007 at http://www.openmopac.net/Minerals.html, near the bottom of the page. David Gallagher CACheResearch.com At 10:09 AM 4/11/2008, Ashish Datt ashish_cares]^[hotmail.com wrote: >Sent to CCL by: "Ashish Datt" [ashish_cares~!~hotmail.com] >Well I wish to model zeolites through quantum mechanical softwares >so I would like to ask for which is the best software to do that Eg >Gaussian or Gamess or something else and also some tips to do that >as I am pretty new in this field. > >thanks >Ashish --=====================_16415140==.ALT Content-Type: text/html; charset="us-ascii" Hi Ashish,

Depending on the size of the zeolite, if you find it is too large or too slow for ab initio methods, you should try semi-empirical. The new PM6 method in MOPAC2007 works well for crystals and uses 'translation vectors' to deal with extended solids (and it's free for academics: http://www.cacheresearch.com/mopac.html ).

There are some example of zeolites structures optimized with MOPAC2007 at http://www.openmopac.net/Minerals.html, near the bottom of the page.

David Gallagher
CACheResearch.com


At 10:09 AM 4/11/2008, Ashish Datt ashish_cares]^[hotmail.com wrote:

Sent to CCL by: "Ashish  Datt" [ashish_cares~!~hotmail.com]
Well I wish to model zeolites through quantum mechanical softwares so I would like to ask for which is the best software to do that Eg Gaussian or Gamess or something else and also some tips to do that as I am pretty new in this field.

thanks
Ashish
--=====================_16415140==.ALT--