From owner-chemistry@ccl.net Tue Mar 20 13:46:01 2007 From: "Cross, Simon scross*tripos.com" To: CCL Subject: CCL: Babel problem (?) Message-Id: <-33854-070320122919-6361-w4Ll1e70p6VeVU7r82WtUg===server.ccl.net> X-Original-From: "Cross, Simon" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 20 Mar 2007 11:29:00 -0500 MIME-Version: 1.0 Sent to CCL by: "Cross, Simon" [scross,+,tripos.com] Hi Martin, SYBYL uses the file $TA_ROOT/tables/SybylAtomMaps to assign atom types using SLN definitions. So you could just add a rule in here to assign phosphate oxygens to your desired O.co2. This should work for dbtranslate command-line (via your script) and also SYBYL itself via the spreadsheet. Simon -----Original Message----- > From: owner-chemistry]=[ccl.net [mailto:owner-chemistry]=[ccl.net] Sent: Monday, March 19, 2007 3:31 PM To: Cross, Simon Subject: CCL: Babel problem (?) Sent to CCL by: Martin Lindh [martinlindh^_^yahoo.se] Thank you for your reply. When I have tried to import the sdf files directly into Sybyl. I get different atom types than if i first convert the files to mol2 format using Babel. For example I get the 03 type on charged oxygens in phosphate groups instead of 0co2. The Babel converted molecules (the one that convert well) seem to dock better in FlexX than if I convert them by importing them directly into Sybyl. I compute charges using the spl script dbcharges so I want to be able to import the molecules into Sybyl. regards Martin --- "Cross, Simon scross{=}tripos.com" skrev: > > Sent to CCL by: "Cross, Simon" [scross_-_tripos.com] > Martin, I'm not sure what the Babel problem is, but > a simple alternative > would be to import the SDF directly into the SYBYL > spreadsheet. Even > simpler would be to select SDF as the ligand input > file format from the > docking interface. > > If it is command-line translation you are after, > SYBYL's dbtranslate > utility should also be available to you. > > Regards, > > Simon > > ------------------------------------ > Dr Simon Cross > Product Manager > Tripos UK Ltd > scross(!)tripos.com > Tel +44 1908 650021 > Mob +44 7980 572278 > Fax +44 1908 650001 > ------------------------------------ > SYBYL, UNITY, and other products are exclusive > property of Tripos & are > protected by trademarks, copyrights, & patents as > appropriate. > > The information in this e-mail is confidential and > may have associated > legal obligations. It is intended for the exclusive > attention of the > addressee stated above and should not be copied or > disclosed to any > other. If you have received this transmission in > error, please contact > the sender. > > > -----Original Message----- > > From: owner-chemistry(!)ccl.net > [mailto:owner-chemistry(!)ccl.net] > Sent: Friday, March 16, 2007 5:16 PM > To: Cross, Simon > Subject: CCL: Babel problem (?) > > > Sent to CCL by: "Martin Lindh" > [martinlindh-$-yahoo.se] > Hi > > I prepare ligands using LigPrep (Maestro). Since I > want to dock these > ligands > in FlexX (Sybyl), I export the ligands from Maestro > as a .sdf file. I > then > use Babel to convert the .sdf file to a multi .mol2 > file. The .mol2 file > is > then imported into Sybyl. > > During this process some(!) of the ligands get > strange mol2 formating. > > Part of a molecule that is translated correctly into > the mol2-file: > [A]ATOM > 1 P1 -7.7746 0.3497 0.1484 P.3 1 <1> > 0.1085 > 2 O1 -7.2207 1.7666 -0.1209 O.2 1 <1> > -0.4607 > 3 O2 -7.9571 -0.5515 -1.0931 O.co2 1 <1> > -0.3575 > > Part of a molecule that is NOT translated correctly > in mol2-file: > > 28 C 14.2736 6.1106 -1.8492 C.ar 0 > UNK0 0.1493 > 29 N 14.3973 5.3090 -0.7250 N.ar 0 > UNK0 -0.2079 > 30 N 13.7198 8.3248 -1.0353 N.pl3 0 > UNK0 -0.3413 > 31 C1* 15.1231 2.8403 -3.4280 C.3 1 > UNK1 0.1683 > 32 O4* 15.0326 3.1353 -4.7858 O.3 1 > UNK1 -0.3456 > 33 C4* 13.7316 2.8114 -5.2536 C.3 1 > UNK1 0.1126 > > Anyone seen this problem and have suggestions of > what to do? > > Thank you in advance > Martinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the a > sign. 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