From owner-chemistry@ccl.net Tue Apr 7 00:58:01 2015 From: "Gulzar Singh gulzar.singh54 * gmail.com" To: CCL Subject: CCL: Torsional Representation Message-Id: <-51219-150407005645-12173-eJX8e3k/uaMacvxBZLCB/g===server.ccl.net> X-Original-From: "Gulzar Singh" Date: Tue, 7 Apr 2015 00:56:43 -0400 Sent to CCL by: "Gulzar Singh" [gulzar.singh54],[gmail.com] Hi I am writing a small tool to generate conformers of any given small molecule. My idea was to get Z-matrix , change torsion, convert to Cartesian and get the conformer. But Z-matrix does not always follow the bonds, it uses the 3D space but not the bonding pattern. Is there any algorithm/tool (open source) which reports all torsions based on their respective four atoms? OR is there any other way to store these torsions? OR any other algorithm/logic (not any ready made tool) to generate conformers? Thank You From owner-chemistry@ccl.net Tue Apr 7 04:49:01 2015 From: "zhoujinming zhou_jim=-=hotmail.com" To: CCL Subject: CCL: Multiple Target Ligand database Message-Id: <-51220-150407044244-2988-fNepvFDDrYlCO3lYNImSxg[#]server.ccl.net> X-Original-From: zhoujinming Content-Type: multipart/alternative; boundary="_c3eefb00-1118-4b57-9d32-a650452094f6_" Date: Tue, 7 Apr 2015 08:42:36 +0000 MIME-Version: 1.0 Sent to CCL by: zhoujinming [zhou_jim././.hotmail.com] --_c3eefb00-1118-4b57-9d32-a650452094f6_ Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: base64 RGVhciBDQ2xlciBXZSB3b3VsZCBsaWtlIHRvIGludHJvZHVjZSBhIERhdGFiYXNlCm9mIE11bHRp cGxlIFRhcmdldCBMaWdhbmQgKE1UTEQpLCB3aGljaCB3YXMgYnVpbHQgdGhyb3VnaCBkYXRhIG1p bmluZyBvZiB0aGUgUHJvdGVpbiBEYXRhIEJhbmsuIFRoZSBNVExEIGNvbnRhaW5zCjEsNzMyIG11 bHRpcGxlLXRhcmdldCBsaWdhbmRzIChNVExzKSB3aGljaCBiaW5kIHRvIDE0LDk5NiBiaW5kaW5n IHNpdGVzIGV4dHJhY3RlZApmcm9tIDEyLDc1OSBQREIgc3RydWN0dXJlcy4gQW1vbmcgTVRMcywg MjIyIGVudHJpZXMgYXJlIGFwcHJvdmVkIGRydWdzIGFuZCAxLDMzNAplbnRyaWVzIGFyZSBkcnVn LWxpa2UgY29tcG91bmRzLiBUaGUgTVRMRCBjb3VsZCBiZSBhY2Nlc3NpYmxlIHRocm91Z2ggaW50 ZXJuZXQgKHd3dy5tdGRjYWRkLmNvbSksIGFuZCBpcyBmcmVlIGZvciBvbmxpbmUKc2VhcmNoaW5n LCBicm93c2luZywgYW5kIGRvd25sb2FkaW5nLiBXZSBob3BlIHRoYXQgdGhlIGRhdGFiYXNlIHdp bGwgYmUgdXNlZnVsCmZvciB5b3UsIGlmIHlvdSBoYXZlIGFueSBxdWVzdGlvbiBvciBhZHZpY2Us IHBsZWFzZSBqdXN0IGNvbnRhY3QgdXMgKHpob3VqaW5taW5nQGltYi5wdW1jLmVkdS5jbikuCk1h bnkgVGhhbmtzLg0KCgoKCgoKSmluTWluZwomIENoYW8gCQkgCSAgIAkJICA= --_c3eefb00-1118-4b57-9d32-a650452094f6_ Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: base64 PGh0bWw+DQo8aGVhZD4NCjxzdHlsZT48IS0tDQouaG1tZXNzYWdlIFANCnsNCm1hcmdpbjowcHg7 DQpwYWRkaW5nOjBweA0KfQ0KYm9keS5obW1lc3NhZ2UNCnsNCmZvbnQtc2l6ZTogMTJwdDsNCmZv bnQtZmFtaWx5Os6iyO3RxbraDQp9DQotLT48L3N0eWxlPjwvaGVhZD4NCjxib2R5IGNsYXNzPSdo bW1lc3NhZ2UnPjxkaXYgZGlyPSdsdHInPjxwIGNsYXNzPSJNc29Ob3JtYWwiPjxzcGFuIGxhbmc9 IkVOLVVTIiBzdHlsZT0ibXNvLWJpZGktZm9udC1zaXplOjEwLjVwdDsKZm9udC1mYW1pbHk6JnF1 b3Q7VGltZXMgTmV3IFJvbWFuJnF1b3Q7LCZxdW90O3NlcmlmJnF1b3Q7Ij5EZWFyIENDbGVyPG86 cD48L286cD48L3NwYW4+PC9wPjxwIGNsYXNzPSJNc29Ob3JtYWwiPjxzcGFuIGxhbmc9IkVOLVVT IiBzdHlsZT0ibXNvLWJpZGktZm9udC1zaXplOjEwLjVwdDsKZm9udC1mYW1pbHk6JnF1b3Q7VGlt ZXMgTmV3IFJvbWFuJnF1b3Q7LCZxdW90O3NlcmlmJnF1b3Q7Ij4mbmJzcDs8L3NwYW4+PC9wPjxw IGNsYXNzPSJNc29Ob3JtYWwiIHN0eWxlPSJtYXJnaW4tYm90dG9tOjEwLjBwdDtsaW5lLWhlaWdo dDoxNTAlO21zby1wYWdpbmF0aW9uOgp3aWRvdy1vcnBoYW4iPjxzcGFuIGxhbmc9IkVOLVVTIiBz dHlsZT0ibXNvLWJpZGktZm9udC1zaXplOjEwLjVwdDtsaW5lLWhlaWdodDoKMTUwJTtmb250LWZh bWlseTomcXVvdDtUaW1lcyBOZXcgUm9tYW4mcXVvdDssJnF1b3Q7c2VyaWYmcXVvdDsiPldlIHdv dWxkIGxpa2UgdG8gaW50cm9kdWNlIGEgRGF0YWJhc2UKb2YgTXVsdGlwbGUgVGFyZ2V0IExpZ2Fu ZCAoTVRMRCksIHdoaWNoIHdhcyBidWlsdCB0aHJvdWdoIGRhdGEgbWluaW5nIG9mIHRoZSBQcm90 ZWluIERhdGEgQmFuay4gVGhlIE1UTEQgY29udGFpbnMKMSw3MzIgbXVsdGlwbGUtdGFyZ2V0IGxp Z2FuZHMgKE1UTHMpIHdoaWNoIGJpbmQgdG8gMTQsOTk2IGJpbmRpbmcgc2l0ZXMgZXh0cmFjdGVk CmZyb20gMTIsNzU5IFBEQiBzdHJ1Y3R1cmVzLiBBbW9uZyBNVExzLCAyMjIgZW50cmllcyBhcmUg YXBwcm92ZWQgZHJ1Z3MgYW5kIDEsMzM0CmVudHJpZXMgYXJlIGRydWctbGlrZSBjb21wb3VuZHMu IFRoZSBNVExEIGNvdWxkIGJlIGFjY2Vzc2libGUgdGhyb3VnaCBpbnRlcm5ldCAoPGEgaHJlZj0i aHR0cDovL3d3dy5tdGRjYWRkLmNvbS8iPnd3dy5tdGRjYWRkLmNvbTwvYT4pLCBhbmQgaXMgZnJl ZSBmb3Igb25saW5lCnNlYXJjaGluZywgYnJvd3NpbmcsIGFuZCBkb3dubG9hZGluZy4gV2UgaG9w ZSB0aGF0IHRoZSBkYXRhYmFzZSB3aWxsIGJlIHVzZWZ1bApmb3IgeW91LCBpZiB5b3UgaGF2ZSBh bnkgcXVlc3Rpb24gb3IgYWR2aWNlLCBwbGVhc2UganVzdCBjb250YWN0IHVzICg8YSBocmVmPSJt YWlsdG86emhvdWppbm1pbmdAaW1iLnB1bWMuZWR1LmNuIj56aG91amlubWluZ0BpbWIucHVtYy5l ZHUuY248L2E+KS4KTWFueSBUaGFua3MuPG86cD48L286cD48L3NwYW4+PC9wPjxwIGNsYXNzPSJN c29Ob3JtYWwiIHN0eWxlPSJtYXJnaW4tYm90dG9tOjEwLjBwdDtsaW5lLWhlaWdodDoxNTAlO21z by1wYWdpbmF0aW9uOgp3aWRvdy1vcnBoYW4iPjxzcGFuIGxhbmc9IkVOLVVTIiBzdHlsZT0ibXNv LWJpZGktZm9udC1zaXplOjEwLjVwdDtsaW5lLWhlaWdodDoKMTUwJTtmb250LWZhbWlseTomcXVv dDtUaW1lcyBOZXcgUm9tYW4mcXVvdDssJnF1b3Q7c2VyaWYmcXVvdDsiPjxicj48L3NwYW4+PC9w PjxwIGNsYXNzPSJNc29Ob3JtYWwiPgoKCgoKCjwvcD48cCBjbGFzcz0iTXNvTm9ybWFsIiBzdHls ZT0ibWFyZ2luLWJvdHRvbToxMC4wcHQ7bGluZS1oZWlnaHQ6MTUwJTttc28tcGFnaW5hdGlvbjoK d2lkb3ctb3JwaGFuIj48c3BhbiBsYW5nPSJFTi1VUyIgc3R5bGU9ImxpbmUtaGVpZ2h0OiAxNTAl OyBmb250LWZhbWlseTogJ1RpbWVzIE5ldyBSb21hbicsIHNlcmlmOyI+SmluTWluZwomYW1wOyBD aGFvPG86cD48L286cD48L3NwYW4+PC9wPiAJCSAJICAgCQkgIDwvZGl2PjwvYm9keT4NCjwvaHRt bD4= --_c3eefb00-1118-4b57-9d32-a650452094f6_--