Re: [rDock-list-def] mol2 format

[Peter S. <pet...@gm...>]

Oh I didn’t even check the SD file. Indeed I also had issues with properties in the SD file if they are formatted in a particular way.
Easiest -> drop them if possible ;)

++

Peter

> On 24 Sep 2019, at 20:41, Markus Metz <me...@gm...> wrote:
> 
> 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... <mailto:pet...@gm...>> wrote:
> Thanks Markus,
> 
> I got lost with the Markus’s here :) 
> 
> 
> 
>> On 23 Sep 2019, at 20:21, Markus Heller <mh...@ad... <mailto: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... <mailto:me...@gm...>> 
>> Sent: Friday, September 20, 2019 4:01 PM
>> To: rdo...@li... <mailto: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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