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
>
>
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