From chemistry-request /at\server.ccl.net Tue Jul 9 03:56:42 2002 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g697ufp32669 for ; Tue, 9 Jul 2002 03:56:41 -0400 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Tue, 9 Jul 2002 09:54:39 +0200 Message-ID: <004e01c2271e$35083e30$3b8506c1: at :cthulhu> From: "Tamas E. Gunda" To: "Luciana Marinelli" , References: <3D29C50E.CCD1338F "-at-" novel7.farmacia.unina.it> Subject: Re: CCL:problem with mol2topdb script Date: Tue, 9 Jul 2002 09:57:00 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Luciana, The sybyl2 file looks quite strange - I mean the atoms and residues are scrambled, bonds between chains etc. The sum of partial charges is -104.18. Is it surely correct? The file was produced by Sybyl, if I understood well. Have you tried to re-read the file into Sybyl? Is it OK then? Regards Dr. Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda&$at$&tigris.klte.hu ----- Original Message ----- From: "Luciana Marinelli" To: Sent: Monday, July 08, 2002 18:59 Subject: CCL:problem with mol2topdb script > hallo, > I am a new AUTODOCK user, I have problem with mol2topdb script. > I am working on a silicon graphics with an operating system: IRIX64 > Release 6. I have download the new one version of autodock. > I have downloaded my protein from PDB and I have added H and charges by > sybyl as you explain in the user guide, than I saved it as mol2 file, > but when I try to run the script that should convert the mol2 file into > the pdbq I have this output: > % mol2topdbq 1L5G.pdb > gawk - Command not found > % > >