Re: [AMBER] Can cpptraj multidihedral use nonbonded atoms?

From: Michael F. Bruist <>
Date: Thu, 28 Feb 2019 23:01:15 +0000


Thank you. This is very useful. I had to modify the script to allow for using different residues in the same dihedral line. This worked for pseudodihedrals:

for residues RES inmask :2-83 i=2;i++
  preRES = $i - 1
  postRES = $i + 1
  dihedral eta$i :$preRES.C4' :$i.P :$i.C4' :$postRES.P out R42etTEST.txt
  dihedral theta$i :$i.C4' :$i.P :$postRES.P :$postRES.C4' out R42etTEST.txt

The script tries to read through the strand break between residues 42 and 43, but because of the missing phosphorus on residue 43, these get skipped avoiding the need for a loop for each strand.

Thanks again.


On 2/21/19, 2:16 PM, "Daniel Roe" <> wrote:

    Currently 'multidihedral' expects dihedrals to be bonded - not sure
    why I made that a limitation, I suppose I could change it...
    In the meantime, you might be able to make use of the new 'for' loop
    syntax (version 18+), which allows you to create loops over mask
    expressions, e.g.
    for residues RES inmask :1-32 i=1;i++
      dihedral dih$i $RES.<atom1> $RES.<atom2> $RES.<atom3> $RES@<atom4>
    Hope this helps,
    On Wed, Feb 20, 2019 at 6:48 PM Michael F. Bruist
    <> wrote:
> I would like to calculate pseudodihedrals in nucleic acids. I can get the values using the dihedral command; however, that will require a line for every dihedral. I can get multidihedral to work when I use four atoms that are bound consecutively (test:O3’:C3’:C4’:O4’:0). However, when even one atom is not bonded to the others (test:O3’:C3’:C4’:O5’:0) I get an error “No dihedrals selected for topology RNA42_5K_WAT.parm7“. Is there a way to use multidihedral for pseudodihedrals in which the atoms are not bonded together?
> Mike Bruist
> Department of Chemistry & Biochemistry
> University of the Sciences
> Philadelphia, PA 19104-4495
> _______________________________________________
> AMBER mailing list
    AMBER mailing list

AMBER mailing list
Received on Thu Feb 28 2019 - 15:30:02 PST
Custom Search