Re: [rDock-list-def] mol2 format

[Markus M. <me...@gm...>]

Hello again:
So I can confirm that the property fields in my sd file where the culprits.
Thank you to everybody chiming in!!
Best,
Markus

On Tue, Sep 24, 2019 at 10:18 AM Peter Schmidtke <pet...@gm...>
wrote:

> Thanks Markus,
>
> I got lost with the Markus’s here :)
>
>
>
> On 23 Sep 2019, at 20:21, Markus Heller <mh...@ad...> wrote:
>
> Hi Markus,
>
> I typically use UCSF’s Dock Prep tool.  Usually works pretty well.
>
> Are you able to share an example of a protein file that fails?
>
> Markus
>
> *From:* Markus Metz <me...@gm...>
> *Sent:* Friday, September 20, 2019 4:01 PM
> *To:* rdo...@li...
> *Subject:* [rDock-list-def] mol2 format
>
> Hello all:
> I am trying to convert my protein to mol2 format and I have tried the
> following:
> a) converted via maestro
> b) used openbabel
> c) used chimera
> d) visually tried to pinpoint where my mol2 file differs from tutorial
> examples.
>
> In every case I failed to run the rbcavity command.
> The best error message I am getting is
> 'Corrupted MOL2 file: not enough fields in SUBSTRUCTURE'.
>
> I can find no difference between the tutorial example and the mol2 file
> created.
> Of course rbcavity works with the tutorial files.
>
> How are you performing the mol2 conversion?
> Kindly let me know,
> Markus
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