Have you visualized the structure to see if it was wrapped? Meaning the
ligand might have already been wrapped if it moved past the box boundary.
On Wed, Sep 11, 2024, 12:56 PM Debarati DasGupta via AMBER <
amber.ambermd.org> wrote:
> Hi experts.
>
> When using the distance command ( I have kept the imaging to off) I am
> not sure if the distance masks are being read correctly, I want to
> calculate the distance between the O22 atom of RES ligand to the N6 atom
> of the adenine and I am not sure if this is working. The distances on pymol
> are in the range of ~2 to 3 angstroms but when I open the dat file it is ~
> 60 angstroms or more.
>
> Secondly I wanted to use the first frame as reference instead of using the
> solvated initial setup.pdb file but when I plugged in "reference first" it
> did not like me either.
>
> Any suggestions on what I am missing ?
>
>
> cpptraj command I am using after loading the traj and stripping water and
> ions:
>
> distance d1 :RES.O22 :3.N6 noimage reference out d1_ligand.dat
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Received on Wed Sep 11 2024 - 10:30:01 PDT
