From owner-chemistry@ccl.net Mon May 4 04:40:00 2009 From: "Vincent.Leroux : loria.fr" <owner-chemistry .. server.ccl.net> To: CCL Subject: CCL: Docking Problem Message-Id: <-39223-090504042153-4963-iNIp5ioffPjwO3lCiVzB6Q .. server.ccl.net> X-Original-From: Vincent.Leroux##loria.fr Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Mon, 04 May 2009 10:21:30 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent.Leroux|,|loria.fr Hi, It is difficult to give you a precise answer as you do not mention the =20 software you are using... Anyway I understood that you are using two distinct =20 minimization/docking techniques but both driven by the same scoring =20 function. I presume that they only differ regarding the degree of =20 conformational sampling that is being performed, so they have a =20 different computational time vs. relevance balance, and provide =20 different results across a given dataset. However, in the case of an =20 "easy guess" (for example, with a "rigid" ligand), both might be =20 equivalent and converge to the same result, this is perfectly normal. For one compound, two distinct methods are giving the same prediction, =20 so this prediction has a greater chance of being good compared to all =20 the other cases in which the two methods are not in agreement. =20 However, if one of the methods is consistantly giving you better =20 docking scores across your dataset, you might obviously decide not to =20 waste anymore time on the other one for forthcoming docking =20 calculations. VL "Kshatresh Dutta Dubey kshatresh],[gmail.com" =20 <owner-chemistry _ ccl.net> a =C3=A9crit=C2=A0: > Dear Vincent, > Firstly thanks for reply, in my previous question i got different docking > score by docking other ligands in virtual and induced fit. The docking > scores are similar for only a particular ligand. > On Thu, Apr 30, 2009 at 5:25 PM, Vincent.Leroux[A]loria.fr < > owner-chemistry a ccl.net> wrote: > >> >> Sent to CCL by: Vincent.Leroux(0)loria.fr >> Probably that you ended up with the same docked conformation in both case= s. >> >> >> "Kshatresh Dutta Dubey kshatresh . gmail.com" <owner-chemistry|,|ccl.net> >> a =C3=A9crit : >> >> Dear subscribers , >>> i have docked a ligand into a protein by both virtual docking as well a= s >>> induced fit and got same docking score. What does this result >>> signifiy????? >>> >>> thanks in advance >>> Kshatresh dutta dubey >>> >> From owner-chemistry@ccl.net Mon May 4 09:16:00 2009 From: "Niels Johan Christensen njc:life.ku.dk" <owner-chemistry|*|server.ccl.net> To: CCL Subject: CCL:G: Counterpoise corrected isotropic shieldings in g03 Message-Id: <-39224-090504091258-19441-VYyAPpYh18JHVmoLl/4ALA|*|server.ccl.net> X-Original-From: "Niels Johan Christensen" <njc^-^life.ku.dk> Date: Mon, 4 May 2009 09:12:53 -0400 Sent to CCL by: "Niels Johan Christensen" [njc#life.ku.dk] Dear Everyone. I am in doubt about how to obtain the counterpoise corrected isotropic shieldings for my dimeric system from the output reported by g03. Five blocks of istropic shieldings are reported in the .log file (viz below) -- but how should these data be combined to produce the counterpoise corrected isotropic shieldings? Best regards Niels 1 C Isotropic = 114.9749 Anisotropy = 25.6743 2 C Isotropic = 135.0906 Anisotropy = 25.4112 ... Counterpoise: doing DCBS calculation for fragment 1 NewBq=T 1 C Isotropic = 114.0190 Anisotropy = 26.4490 2 C Isotropic = 135.1089 Anisotropy = 26.7381 ... Counterpoise: doing DCBS calculation for fragment 2 NewBq=T 1 C Isotropic = 0.4941 Anisotropy = 3.0291 2 C Isotropic = 0.3456 Anisotropy = 2.3343 ... Counterpoise: doing MCBS calculation for fragment 1 1 C Isotropic = 114.1432 Anisotropy = 26.4755 2 C Isotropic = 135.1009 Anisotropy = 26.7568 ... Counterpoise: doing MCBS calculation for fragment 2 24 C Isotropic = 73.0508 Anisotropy = 184.3264 25 C Isotropic = 73.0846 Anisotropy = 184.3008 ... From owner-chemistry@ccl.net Mon May 4 13:15:01 2009 From: "IOANA OPRISIU ioana.oprisiu+/-ulp.u-strasbg.fr" <owner-chemistry^server.ccl.net> To: CCL Subject: CCL: Boiling temperature data Message-Id: <-39225-090504113346-24436-L5MbiNvLYfx2kp/G8NBI0Q^server.ccl.net> X-Original-From: "IOANA OPRISIU" <ioana.oprisiu:ulp.u-strasbg.fr> Date: Mon, 4 May 2009 11:33:42 -0400 Sent to CCL by: "IOANA OPRISIU" [ioana.oprisiu]=[ulp.u-strasbg.fr] Hello, I'm looking for data sets (desirable SDF format or smiles) containing normal boiling temperature, in order to develop QSPR models using ISIDA descriptors. Thank you in advance. IOANA OPRISIU PhD. Student in Chemoinformatics From owner-chemistry@ccl.net Mon May 4 16:09:00 2009 From: "Martin Mueller martin.mueller%a%ime.fraunhofer.de" <owner-chemistry[A]server.ccl.net> To: CCL Subject: CCL: PCDD, PBDE, PCDF congeners Message-Id: <-39226-090504115609-26109-yOKo9hHDmiGySfoE5RpwRQ[A]server.ccl.net> X-Original-From: Martin Mueller <martin.mueller[]ime.fraunhofer.de> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 04 May 2009 17:19:24 +0200 MIME-Version: 1.0 Sent to CCL by: Martin Mueller [martin.mueller:ime.fraunhofer.de] Hi, I'm looking for CAS-numbers for (all?) congeners of polychlorinated dibenzodioxins (PCDD), polychlorinated dibenzofuranes (PCDF), polybrominated diphenylethers (PBDE) I found a table for the complete set of PCB congeners: http://www.epa.gov/osw/hazard/tsd/pcbs/pubs/congenertable.pdf it would be nice, to have similar for the other compound classes. The best I found up to now (but not complete) http://www.inchem.org/documents/ehc/ehc/ehc205.htm#SubSectionNumber:2.2.2 Anyone an idea? Thanks in advance Martin From owner-chemistry@ccl.net Mon May 4 18:36:01 2009 From: "Syed Tarique Moin tarisyed^_^yahoo.com" <owner-chemistry=-=server.ccl.net> To: CCL Subject: CCL:G: QM/MM and copper Message-Id: <-39227-090504182646-26878-qlcZUYMqvyBN8ftngHamMw=-=server.ccl.net> X-Original-From: "Syed Tarique Moin" <tarisyed_+_yahoo.com> Date: Mon, 4 May 2009 18:26:42 -0400 Sent to CCL by: "Syed Tarique Moin" [tarisyed-$-yahoo.com] Dear CCl users, I am trying to simulate the copper containing metalloprotein. For the QM/MM, i am using the hybrid software method incorporating Gaussian as the QM source and Amber as a MM using pupil package interface. Can anybody tell me free package other than pupil for interfacing these two programs and the good basis set for the copper (II) coordinated with amino acids. Regards From owner-chemistry@ccl.net Mon May 4 19:10:00 2009 From: "Tom Stockfisch t.stockfisch#cox.net" <owner-chemistry * server.ccl.net> To: CCL Subject: CCL: PCDD, PBDE, PCDF congeners Message-Id: <-39228-090504190102-19535-QUMMMr75MM7wzm02Pim1ig * server.ccl.net> X-Original-From: Tom Stockfisch <t.stockfisch[#]cox.net> Content-Type: multipart/alternative; boundary=Apple-Mail-1--972195678 Date: Mon, 4 May 2009 15:18:12 -0700 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Tom Stockfisch [t.stockfisch:_:cox.net] --Apple-Mail-1--972195678 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi Martin - I believe you can get this number easily for free by using http:// www.emolecules.com. Tom Tom Stockfisch t.stockfisch_-_cox.net http://www.tstockfisch.com 760-497-4108 mobile On May 4, 2009, at 8:19 AM, Martin Mueller martin.mueller%a% ime.fraunhofer.de wrote: > > Sent to CCL by: Martin Mueller [martin.mueller:ime.fraunhofer.de] > Hi, > > I'm looking for CAS-numbers for (all?) congeners of polychlorinated > dibenzodioxins (PCDD), polychlorinated dibenzofuranes (PCDF), > polybrominated diphenylethers (PBDE) > > I found a table for the complete set of PCB congeners: > http://www.epa.gov/osw/hazard/tsd/pcbs/pubs/congenertable.pdf > > it would be nice, to have similar for the other compound classes. > > The best I found up to now (but not complete) > http://www.inchem.org/documents/ehc/ehc/ehc205.htm#SubSectionNumber: > 2.2.2 > > Anyone an idea? > > Thanks in advance > > Martin > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changehttp://www.ccl.net/chemistry/ > sub_unsub.shtmlConferences: http://server.ccl.net/ > chemistry/announcements/conferences/> > --Apple-Mail-1--972195678 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 <html><body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; = -webkit-line-break: after-white-space; "> Hi Martin -<div><br></div><div>I believe you can get this number easily = =A0for free by using <a = href=3D"http://www.emolecules.com">http://www.emolecules.com</a>.</div><di= v><br></div><div>Tom</div><div><br><div> <span class=3D"Apple-style-span" = style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: = Helvetica; font-size: 16px; font-style: normal; font-variant: normal; = font-weight: normal; letter-spacing: normal; line-height: normal; = orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; = white-space: normal; widows: 2; word-spacing: 0px; = -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: = 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: = auto; -webkit-text-stroke-width: 0; "><span class=3D"Apple-style-span" = style=3D"border-collapse: separate; -webkit-border-horizontal-spacing: = 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); = font-family: Helvetica; font-size: 14px; font-style: normal; = font-variant: normal; font-weight: normal; letter-spacing: normal; = line-height: normal; -webkit-text-decorations-in-effect: none; = text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; = orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span = class=3D"Apple-style-span" style=3D"border-collapse: separate; = -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: = 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; = font-style: normal; font-variant: normal; font-weight: normal; = letter-spacing: normal; line-height: normal; = -webkit-text-decorations-in-effect: none; text-indent: 0px; = -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; = white-space: normal; widows: 2; word-spacing: 0px; "><div>Tom = Stockfisch</div><div><a = href=3D"mailto:t.stockfisch_-_cox.net">t.stockfisch_-_cox.net</a></div><div><a= = href=3D"http://www.tstockfisch.com">http://www.tstockfisch.com</a></div><d= iv>760-497-4108 mobile</div><div><br = class=3D"khtml-block-placeholder"></div><br = class=3D"Apple-interchange-newline"></span></span></span><br = class=3D"Apple-interchange-newline"> </div><br><div><div>On May 4, 2009, = at 8:19 AM, Martin Mueller martin.mueller%a%ime.fraunhofer.de = wrote:</div><br class=3D"Apple-interchange-newline"><blockquote = type=3D"cite"><div style=3D"margin-top: 0px; margin-right: 0px; = margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; ">Sent to CCL by: Martin Mueller = [martin.mueller:ime.fraunhofer.de]</div><div style=3D"margin-top: 0px; = margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi,</div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; min-height: 14px; "><br></div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I'm = looking for CAS-numbers for (all?) congeners of polychlorinated = dibenzodioxins (PCDD), polychlorinated dibenzofuranes (PCDF), = polybrominated diphenylethers (PBDE)</div><div style=3D"margin-top: 0px; = margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: = 14px; "><br></div><div style=3D"margin-top: 0px; margin-right: 0px; = margin-bottom: 0px; margin-left: 0px; ">I found a table for the complete = set of PCB congeners:</div><div style=3D"margin-top: 0px; margin-right: = 0px; margin-bottom: 0px; margin-left: 0px; "><a = href=3D"http://www.epa.gov/osw/hazard/tsd/pcbs/pubs/congenertable.pdf">htt= p://www.epa.gov/osw/hazard/tsd/pcbs/pubs/congenertable.pdf</a></div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; min-height: 14px; "><br></div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">it would = be nice, to have similar for the other compound classes.</div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; min-height: 14px; "><br></div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">The best = I found up to now (but not complete)</div><div style=3D"margin-top: 0px; = margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a = href=3D"http://www.inchem.org/documents/ehc/ehc/ehc205.htm#SubSectionNumbe= r:2.2.2">http://www.inchem.org/documents/ehc/ehc/ehc205.htm#SubSectionNumb= er:2.2.2</a></div><div style=3D"margin-top: 0px; margin-right: 0px; = margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; ">Anyone an idea?</div><div style=3D"margin-top: 0px; = margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: = 14px; "><br></div><div style=3D"margin-top: 0px; margin-right: 0px; = margin-bottom: 0px; margin-left: 0px; ">Thanks in advance</div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; min-height: 14px; "><br></div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; = ">Martin</div><div style=3D"margin-top: 0px; margin-right: 0px; = margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; min-height: 14px; "><br></div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; = min-height: 14px; "><br></div><div style=3D"margin-top: 0px; = margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-=3D This is = automatically added to each message by the mailing script =3D-</div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; ">To recover the email address of the author of the = message, please change</div><div style=3D"margin-top: 0px; margin-right: = 0px; margin-bottom: 0px; margin-left: 0px; ">the strange characters on = the top line to the _-_ sign. You can also</div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">look up = the X-Original-From: line in the mail header.</div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; min-height: 14px; "><br></div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">E-mail = to subscribers: <a href=3D"mailto:CHEMISTRY_-_ccl.net">CHEMISTRY_-_ccl.net</a>= or use:</div><div style=3D"margin-top: 0px; margin-right: 0px; = margin-bottom: 0px; margin-left: 0px; "><span = class=3D"Apple-converted-space">=A0=A0 =A0 </span><a = href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.ne= t/cgi-bin/ccl/send_ccl_message</a></div><div style=3D"margin-top: 0px; = margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: = 14px; "><br></div><div style=3D"margin-top: 0px; margin-right: 0px; = margin-bottom: 0px; margin-left: 0px; ">E-mail to administrators: <a = href=3D"mailto:CHEMISTRY-REQUEST_-_ccl.net">CHEMISTRY-REQUEST_-_ccl.net</a> = or use</div><div style=3D"margin-top: 0px; margin-right: 0px; = margin-bottom: 0px; margin-left: 0px; "><span = class=3D"Apple-converted-space">=A0=A0 =A0 </span><a = href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.ne= t/cgi-bin/ccl/send_ccl_message</a></div><div style=3D"margin-top: 0px; = margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: = 14px; "><br></div><div style=3D"margin-top: 0px; margin-right: 0px; = margin-bottom: 0px; margin-left: 0px; ">Subscribe/Unsubscribe:<span = class=3D"Apple-converted-space">=A0 =A0 =A0 </span><a = href=3D"http://www.ccl.net/chemistry/sub_unsub.shtml">http://www.ccl.net/c= hemistry/sub_unsub.shtml</a></div><div style=3D"margin-top: 0px; = margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: = 14px; "><br></div><div style=3D"margin-top: 0px; margin-right: 0px; = margin-bottom: 0px; margin-left: 0px; ">Before posting, check wait time = at: <a href=3D"http://www.ccl.net">http://www.ccl.net</a></div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; min-height: 14px; "><br></div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Job: <a = href=3D"http://www.ccl.net/jobs">http://www.ccl.net/jobs</a> = Conferences: <a = href=3D"http://server.ccl.net/chemistry/announcements/conferences/">http:/= /server.ccl.net/chemistry/announcements/conferences/</a></div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; min-height: 14px; "><br></div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Search = Messages: <a = href=3D"http://www.ccl.net/chemistry/searchccl/index.shtml">http://www.ccl= .net/chemistry/searchccl/index.shtml</a></div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; = min-height: 14px; "><br></div><div style=3D"margin-top: 0px; = margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">If your mail = bounces from CCL with 5.7.1 error, check:</div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span = class=3D"Apple-converted-space">=A0=A0 =A0 </span><a = href=3D"http://www.ccl.net/spammers.txt">http://www.ccl.net/spammers.txt</= a></div><div style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: = 0px; margin-left: 0px; min-height: 14px; "><br></div><div = style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; = margin-left: 0px; ">RTFI: <a = href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.cc= l.net/chemistry/aboutccl/instructions/</a></div><div style=3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; = min-height: 14px; "><br></div><div style=3D"margin-top: 0px; = margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: = 14px; "><br></div> </blockquote></div><br></div></body></html>= --Apple-Mail-1--972195678--