On Mon, Apr 18, 2016, Brett wrote:
>
> Suppose my protein complex contains 4 identical subunits, each identical
> contains a ligand. Although the 4 ligands of every subunit are same
> compound (for example in each subunit it contains a cAMP), I find from
> the relative coordinate view the 4 cAMPs are not identical (or there is
> a slignt rmsd between each cAMP). In this way should I have antechamber
> to produce the ligand files base on the pdb of 1 single cAMP and then
> just tell AMBER there are 4 identical cAMPs for md, or I should produce
> the ligand files from every cAMP for md?
Antechamber doesn't know anything about the environment that the ligands will
have once they are bound to the protein. So you can use a single mol2 and
frcmod file.
...dac
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Received on Mon Apr 18 2016 - 04:30:03 PDT
