Re: [rDock-list-def] mol2 format

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

Thanks Peter:
Actually I think I found the issue.
Could you please do me a favor and go into the ligand sd file and remove
all property fields and try rerunning the cavity calculation?
Thank you so much for your time!
Markus

On Tue, Sep 24, 2019 at 9:53 AM Peter Schmidtke <pet...@gm...>
wrote:

> I personally get a Segfault with your input files. Probably yet another
> problem for now.
> On 3decision.discngine.cloud we use rdock behind the scenes and rbcavity
> runs fine.
>
> There we use pdb2pqr + open babel . I attach the sample mol2 that works
> over here.
>
> I suspect your section :
>
> 1 ALA1B  to mess things up maybe?
>
> I don’t have maestro, so cannot check that out in detail, but I suspect
> the mol2 format is not standard.
>
> Could you try to drop all alternates, unnecessary chains etc to test this?
>
> Peter
>
>
>
> On 24 Sep 2019, at 17:38, Markus Metz <me...@gm...> wrote:
>
> Dear Markus and Peter:
> Apologies for the delay!
>
> Here is an example:
> I downloaded 1oyt for rcsb.org and processed it within maestro using the
> prep wizard.
> And the ligand is also attached. I exported this ligand in mol format from
> maestro and converted it via obabel to sdf.
>
> According to the manual rdock reads the atom name, cart cords and tripos
> atom types. So all the other info is discarded?
> Otherwise may be the numbering of the residues in the ATOM section is
> different.
>
> Best,
> Markus
>
> On Tue, Sep 24, 2019 at 8:26 AM Peter Schmidtke <pet...@gm...>
> wrote:
>
>> Hey Markus,
>>
>> any chance you can share the faulty mol2 files?
>> I personally use open babel to do that.
>>
>> ++
>>
>> Peter
>>
>> > On 21 Sep 2019, at 01:00, Markus Metz <me...@gm...> wrote:
>> >
>> > 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
>> > _______________________________________________
>> > rDock-list-def mailing list
>> > rDo...@li...
>> > https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>>
>> <1oyt_min_prot.mol2><1oyt_min_lig.sd>
>
>
>