Re: [rDock-list-def] mol2 format

[Markus H. <mh...@ad...>]

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