[AMBER] Can cpptraj multidihedral use nonbonded atoms?

From: Michael F. Bruist <m.bruist.usciences.edu>
Date: Wed, 20 Feb 2019 23:48:29 +0000

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

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Received on Wed Feb 20 2019 - 16:00:03 PST
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