On Mon, May 02, 2016, Brett wrote:
>
> When I read the AMBER on-line tutorial on antechamber (the Sustiva
> example), I find the antechamber will determine the value of the
> charge of the ligand.
This is not true: can you say exactly where in the tutorial you got that
impression? You must tell antechamber the net charge of the molecule, unless
it is neutral (which is the default).
> But for some ligand, for example ADP (adenosine
> phosphate), if the H has been added by pdbtools (phenix), it will
> contain -3 charges. But if the H has been added by chimera, it will
> contain -2 charges. For antechamber, do I nee to add the H before I get
> the mol2 file by antechamber? And how many charges antechamber will give
> for ADP?
You must indeed add hydrogens before running antechamber. The net charge
that you use (via the -nc flag) depends on how many hydrogens have been added.
There is often no one "correct" answer, especially for phosphates, which
generally exist in more than one protonation state near neutral pH.
...dac
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Received on Mon May 02 2016 - 07:30:03 PDT
