The tutorial Marc suggested is a good starting point. But beware of using reduce to add hydrogens to the ligand. Last time I tried it
reduce ligand.pdb > ligand_h.pdb
didn't work. I get round this problem by adding hydrogens to the ligand by means of other programs (e.g. Chimera).
Regards
George
On May 24, 2012, at 1:40 PM, Marc van der Kamp wrote:
> 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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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
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Received on Thu May 24 2012 - 06:30:03 PDT
