Re: [Open Babel] SDF to PDB
Hi Daniel, Can you be more specific than just won't work? Like, it won't install? It won't run? It runs but doesn't give the right answer? It runs but gives an error message? If you can tell us exactly what you're doing, what happened, and what you expected to happen (and attach relevant files, if any), I'm sure there's an answer. Craig On Tue, Mar 18, 2014 at 8:36 AM, Daniel Rodriguez Elvira d_r_elv...@hotmail.com wrote: I am trying to convert a SDF file to PDB using Babel, but it just won't work. I am just getting started on using Linux and into the docking world. So a step by step explanation would be most appreciated. regards, Dennis -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SDF to PDB
Craig, You are right, I should be more specific, sorry. I installed the apt just fine, but when I type babel example.sdf example.pdb the following message appears: Cannot open CID_969516.sdf 0 molecules converted 1 errors I tried it both by having the file in my flash-drive and my hard-drive. I am trying to convert this file into PDB so I can do some docking exercises in AutoDock and Pymol Daniel Date: Tue, 18 Mar 2014 09:11:43 -0700 Subject: Re: [Open Babel] SDF to PDB From: cja...@emolecules.com To: d_r_elv...@hotmail.com CC: openbabel-discuss@lists.sourceforge.net Hi Daniel, Can you be more specific than just won't work? Like, it won't install? It won't run? It runs but doesn't give the right answer? It runs but gives an error message? If you can tell us exactly what you're doing, what happened, and what you expected to happen (and attach relevant files, if any), I'm sure there's an answer. Craig On Tue, Mar 18, 2014 at 8:36 AM, Daniel Rodriguez Elvira d_r_elv...@hotmail.com wrote: I am trying to convert a SDF file to PDB using Babel, but it just won't work. I am just getting started on using Linux and into the docking world. So a step by step explanation would be most appreciated. regards, Dennis -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SDF to PDB
On Tue, Mar 18, 2014 at 9:19 AM, Daniel Rodriguez Elvira d_r_elv...@hotmail.com wrote: Craig, You are right, I should be more specific, sorry. I installed the apt just fine, but when I type babel example.sdf example.pdb the following message appears: Cannot open CID_969516.sdf 0 molecules converted 1 errors That doesn't seem quite right. Why is it complaining about CID_969516.sdf when you typed example.sdf? If what you mean is that you typed: babel CID_969516.sdf CID_969516.pdb then the error makes more sense. You probably don't have permission to open the file. Try ls -l CID_969516.sdf to see the permissions and ownership. Type more CID_969516.sdf to see if you can read the file's contents. This sounds like a Linux file-permission problem, not an OpenBabel problem. Craig I tried it both by having the file in my flash-drive and my hard-drive. I am trying to convert this file into PDB so I can do some docking exercises in AutoDock and Pymol Daniel -- Date: Tue, 18 Mar 2014 09:11:43 -0700 Subject: Re: [Open Babel] SDF to PDB From: cja...@emolecules.com To: d_r_elv...@hotmail.com CC: openbabel-discuss@lists.sourceforge.net Hi Daniel, Can you be more specific than just won't work? Like, it won't install? It won't run? It runs but doesn't give the right answer? It runs but gives an error message? If you can tell us exactly what you're doing, what happened, and what you expected to happen (and attach relevant files, if any), I'm sure there's an answer. Craig On Tue, Mar 18, 2014 at 8:36 AM, Daniel Rodriguez Elvira d_r_elv...@hotmail.com wrote: I am trying to convert a SDF file to PDB using Babel, but it just won't work. I am just getting started on using Linux and into the docking world. So a step by step explanation would be most appreciated. regards, Dennis -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
