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

From: Daniel Roe <>
Date: Thu, 21 Feb 2019 14:16:25 -0500


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

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Received on Thu Feb 21 2019 - 11:30:04 PST
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