Maybe I didn't understand what is exactly what you need, but if all
you want is an angle for certain structures or trajectories, I'd
suggest you do it with VMD or Jmol. It's much more comfortable.
Best,
Diego
Quoting MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>:
> Hi,
> I need calculated dihedral angles using AMBER scripts in my
> protein-ligand complexes.
> Previously, I calculated this angles in my ligands (saccharides)
> through cpptraj with next script (these molecular dynamics were
> launched in cluster with AMBER 16):
>
> dihedral Glc2_H1-C1-C2-H2 :2.H1 :2.C1 :2.C2 :2.H2 out Glc2_H1-C1-C2-H2.out
> dihedral Glc2_H2-C2-C3-H3 :2.H2 :2.C2 :2.C3 :2.H3 out Glc2_H2-C2-C3-H3.out
> dihedral Glc2_H3-C3-C4-H4 :2.H3 :2.C3 :2.C4 :2.H4 out Glc2_H3-C3-C4-H4.out
> dihedral Glc2_H4-C4-C5-H5 :2.H4 :2.C4 :2.C5 :2.H5 out Glc2_H4-C4-C5-H5.out
>
> dihedral GalNac3_H1-C1-C2-H2 :3.H1 :3.C1 :3.C2 :3.H2 out
> GalNac3_H1-C1-C2-H2.out
> dihedral GalNac3_H2-C2-C3-H3 :3.H2 :3.C2 :3.C3 :3.H3 out
> GalNac3_H2-C2-C3-H3.out
> dihedral GalNac3_H3-C3-C4-H4 :3.H3 :3.C3 :3.C4 :3.H4 out
> GalNac3_H3-C3-C4-H4.out
> dihedral GalNac3_H4-C4-C5-H5 :3.H4 :3.C4 :3.C5 :3.H5 out
> GalNac3_H4-C4-C5-H5.out
>
>
> It was launched: cpptraj -i distance.in -p disaccharide.top and
> obtained the files.out.
> Now, I want calculated the same in the complexes protein-saccharide,
> but this script not work (these simulations were launched in other
> cluster with AMBER 11), and I don't know if this is the problem... so
> any help will appreciate .
>
>
>
>
> Thanx so much
>
>
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Received on Wed Jan 30 2019 - 08:30:03 PST
