Hi
2 pointers:
1) in what you call is your script, there is no 'trajin' and you don't
specify a -y flag in your command. So are you sure you are parsing a
trajectory to be analyzed?
2) you say problems arise when analyzing the protein-saccharide
simulations. Are you sure the residue numbers of your saccharides are 2 and
3? In your atom mask you have for example ':2.H1' which searches for atom
H1 in residue 2. If your saccharides changed residue number by adding the
protein, cpptraj won't find the correct atoms.
Actual output of the error would be helpful, because otherwise we're just
guessing what might be wrong.
Kind regards
CA Mattelaer
Op wo 30 jan. 2019 17:04 schreef <diego.soler.uam.es:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
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Received on Wed Jan 30 2019 - 08:30:03 PST
