On Wed, Sep 28, 2016, Elisa Pieri wrote:
>
> I have a PDB containing a protein inserted in a membrane, plus two water
> layers, yielding a "cubic" unit. Here the tleap input I used to get the
> parameters:
>
> source leaprc.constphRET (<-- a customized leaprc for the cromophore)
> source leaprc.lipid14
> loadAmberParams frcmod.ionsjc_tip3p
> monomer = loadPDB monomer.pdb
> setBox monomer "vdw"
Are you sure you want this command? Don't you already know the size of the
box to use? If so, replace the above with this:
set monomer box { a b c}
where a b c are the sizes of the box in your model. Then, as Jason said,
use periodic boundary conditions at all stages of subsequent calculations.
....good luck....dac
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Received on Thu Sep 29 2016 - 12:00:03 PDT
