From chemistry-request@server.ccl.net Tue Sep 26 11:29:52 2000 Received: from server.biokemi.su.se (server.biokemi.su.se [130.237.179.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA06182 for ; Tue, 26 Sep 2000 11:29:51 -0400 Received: from mail.biokemi.su.se (unverified [130.237.179.175]) by server.biokemi.su.se (EMWAC SMTPRS 0.83) with SMTP id ; Tue, 26 Sep 2000 17:32:48 +0200 Sender: zhang@ccl.net Message-ID: <39D0BFAE.6DCADBC8@mail.biokemi.su.se> Date: Tue, 26 Sep 2000 17:24:30 +0200 From: Xiao-Ping Zhang Reply-To: zhang@biokemi.su.se X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-12 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Autodock: autotors References: <39CB8291.73206A75@mail.biokemi.su.se> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, A few days ago, I posted a question about "autotors" in autodock package (see following). I haven't got any answer yet. But I found that this problem is related to the presence of cysteine residue in the ligand peptide. I tried the "autotors" from both autodock 3.0 and 3.0.5 release. It seems that the "autotors" on my machine (PC Linux) can not handle the -SH group of cysteine. "Autotors" either crashes or skips the atoms in -SH group and add a symbol (^) in a few places and move the ENDROOT to end of the line which contains the symbol. Off course you can not get a grid map file for S atom if you don't edit the new pdbq file. I wonder if this is a bug in "autotors" code or the problem of my compilation? Does any body tried to run autotors with a ligand which contains S atom or -SH group? Any suggestions are highly appreciated. Sincerely yours, Xiao-Ping Zhang Xiao-Ping Zhang wrote: > > Dear autodock experts, > > I got a problem to run "autotors" on some of my peptide > models (the conformation of the peptide might not be > realistic, but everyone was refined in molecular modeling > program). I got the following error message: > > mol2flag = 0 > hflag = 1 > offset = 70 > aflag = 1 > bflag = 1 > > bnd format:94 records read in > unable to attach all pieces of bond data > > Does anybody encountered a similar problem before? How to > solve it? > > Thank you advance for any suggestions. > > Have a nice weekend? > > Sincerely, > > Zhang > > ****************************** > Xiao-Ping Zhang > Department of Biochemistry > Arrhenius Laboratories of Natural Sciences > Stockholm Universities > 106 91 Stockholm > Sweden > > Phone: 046-08-162472 /162582 > Fax: 046-08-153679 > e-mail: zhang@biokemi.su.se > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang@biokemi.su.se