From chemistry-request@server.ccl.net Sat Jul 7 10:30:01 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f67ETn512204 for ; Sat, 7 Jul 2001 10:29:52 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 15It5L-000482-00; Sat, 07 Jul 2001 16:29:27 +0200 Received: from vejas.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id QAA13340 for ; Sat, 7 Jul 2001 16:39:27 +0200 (GMT) Date: Sat, 7 Jul 2001 04:29:00 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <1509032055.20010707042900@vaidila.vdu.lt> To: "ccl ccl" Subject: CCL: Fe atom in ligand for AutoDock ????? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I try to dock ligand with Fe. After making Grid Parameter File (*.gpf), there is no Fe atom map (Fe atom type was written as "f" in PDBQ file). My AutoDock version is 3.0.5. Why there is no f map (Fe) assigned in automatic generated GPF ? I have tried use spare atom type as X or M, but the result was the same. AutoDock homepage tells there is prepared f type for Fe .... What is wrong ? How can I model Fe in ligand ??? Have a nice day Arturas Z From chemistry-request@server.ccl.net Sat Jul 7 12:20:34 2001 Received: from laplace.quimica.ufpr.br ([200.17.215.88]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f67GKX513181 for ; Sat, 7 Jul 2001 12:20:33 -0400 Received: from quimica.ufpr.br (localhost.quimica.ufpr.br [127.0.0.1]) by laplace.quimica.ufpr.br (8.11.3/8.11.1) with ESMTP id f67GKVY74989 for ; Sat, 7 Jul 2001 13:20:32 -0300 (BRT) (envelope-from edulsa@quimica.ufpr.br) Sender: edulsa@laplace.quimica.ufpr.br Message-ID: <3B4736CF.F1323B5C@quimica.ufpr.br> Date: Sat, 07 Jul 2001 13:20:31 -0300 From: Eduardo X-Mailer: Mozilla 4.76 [en] (X11; U; FreeBSD 4.3-STABLE i386) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Looking for ionic radius of Vandium (IV) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Listers Please, where can I find (in digital data bank or press) the ionic radius of Vanadium (IV)? thanks a lot in advance yours Eduardo -- Eduardo Lemos de Sa Dep. Quimica - Universidade Federal do Parana Curitiba - PR - Brazil Box: 19081 - Zip: 81531-990 - Phone: +55(41)361-3300 From chemistry-request@server.ccl.net Sat Jul 7 20:43:54 2001 Received: from unlserve.unl.edu ([129.93.1.130]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f680hs516228 for ; Sat, 7 Jul 2001 20:43:54 -0400 Received: from localhost (jmazlo@localhost) by unlserve.unl.edu (8.9.1a/8.9.2) with SMTP id TAA46784 for ; Sat, 7 Jul 2001 19:26:37 -0500 Date: Sat, 7 Jul 2001 19:26:36 -0500 (CDT) From: Johanna Mazlo To: chemistry@ccl.net Subject: autodock Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCL group, I am a novice with modeling. I am trying to dock an 8 residue peptide to an antibody that will be used for rational mutagensis experiments. I am using autodock3.0. The peptide was produced using the biopolymer menu of SYBYL, adding Essential_Only hydrogens, assigning KollUA partial charges, and saving it as a mol2 file. I followed the "Getting Started" section of the manual. When I run the deftors peptide.mol2, I receive several errors in the .err file: REMARK *** ERROR 1 *** Non-integral total charge (0.404) for residue AMN- 9! REMARK *** ERROR 1 *** Non-integral total charge (0.398) for residue PRO- 1!REMARK *** ERROR 1 *** Non-integral total charge (0.992) for residue ARG- 8! REMARK *** ERROR 1 *** Non-integral total charge (0.236) for residue AMN- 9! REMARK *** ERROR 2 *** Non-integral total charge (-1.034) for residue CXL- 10! REMARK *** ERROR 3 *** Non-integral total charge (1.992) for whole system! I am not quite sure what to do next. I would greatly appreciate your advice. Thank you Johanna Mazlo University of Nebraska Lincoln, NE 68588-0304 jmazlo@unlserve.unl.edu