Hi,
Why are you trying to make a mol2 of the ligand AND the protein in the
first place?
Antechamber is made to deal with just the mol2 of the ligand, NOT the
protein-ligand complex.
Try following a tutorial, e.g.
http://ambermd.org/tutorials/basic/tutorial4b/
Vega ZZ may already create a suitable mol2 of the ligand (when you give it
a pdb of the ligand only), otherwise openbabel would indeed be a good
option.
--Marc
On 24 May 2012 09:24, g t <sketchfoot.gmail.com> wrote:
> hi,
>
> i believe openbabel can convert from mol2 to pdb. i think it will also sort
> the ligand out. win & linux versions are available.
>
> best regards,
> gt
>
> On 22 May 2012 04:46, Chris Chris <alpharecept.yahoo.com> wrote:
>
> > I am trying to convert a mol2 file into a pdb (using Vega ZZ.). I start
> > with test.mol2- which has both the ligand and and the protein- but when I
> > save as a pdb in Vega ZZ (test_vega.pdb), only the protein is written in
> > the pdb and the ligand is not included. I notice that the connect info in
> > the mol2 (test.mol2) comes before the ligand coordinates- does the
> connect
> > information cause the reading to stop? I want to put this complex into
> > antechamber but I have been having problems generating the pdb file for
> the
> > complex.
> >
> > Thanks for any help
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> >
> >
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Received on Thu May 24 2012 - 05:00:02 PDT
