[AMBER] cpptraj

From: MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
Date: Tue, 05 Feb 2019 15:51:05 +0100

Hi all,

I want to calculate torsion angles in my complex. My script is:

trajin /home/cristina/smp-196ptn/md125ns/ptn4rig_vcon.mdcrd
center :1-9 mass origin
image origin center
dihedral phi3-2 :3.H1 :3.C1 :2.O4 :2.C4 out phi3-2.out
dihedral psi3-2 :3.C1 :2.O4 :2.C4 :2.H4 out psi3-2.out
dihedral phi4-3 :2222 :4.C1 :3.O3 :3.C3 out phi4-3.out
dihedral psi4-3 :4.C1 :3.O3 :3.C3 :3.H3 out psi4-3.out
dihedral phi5-4 :5.H1 .2242 :4.O4 :4.C4 out phi5-4.out
dihedral psi5-4 :2242 :4.O4 :4.C4 :4.H4 out psi5-4.out

In dihedral phi5-4 :5.H1 .2242 :4.O4 :4.C4 out phi5-4.out, I had to
write the atom number instead C1, because when I launched the
calculations, it doesn't find this atom.
Now, when I launch the calculations, the files.out are created, but
before appears this:

  7: [dihedral psi5-4 :2242 :4.O4 :4.C4 :4.H4 out psi5-4.out]
         :2242 (3 atoms)
         :4.O4 (1 atoms)
         :4.C4 (1 atoms)
         :4.H4 (1 atoms)
----- [ptn4rig_vcon.mdcrd] (1-5672, 1) -----
  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

My questions are,

1)Why does it appears 3 atoms in :2242? (I checked the file.pdb and
there is a single atom with this number)

2)this format is correct? what is the different if I write .2242 or
:2242 in this line?

Thanks and Regards

AMBER mailing list
Received on Tue Feb 05 2019 - 07:00:03 PST
Custom Search