[AMBER] dihedral angles

From: MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
Date: Wed, 30 Jan 2019 16:49:46 +0100

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
dihedral GalNac3_H2-C2-C3-H3 :3.H2 :3.C2 :3.C3 :3.H3 out
dihedral GalNac3_H3-C3-C4-H4 :3.H3 :3.C3 :3.C4 :3.H4 out
dihedral GalNac3_H4-C4-C5-H5 :3.H4 :3.C4 :3.C5 :3.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 - 08:00:03 PST
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