Date: Fri, 16 Aug 2024 14:52:43 +0000
Hi all,
I'm working with a nucleic acid (tRNA) simulation, and I wish to measure
the two pseudo-torsions "eta" and "theta" that simplify the analysis of
nucleic acid backbone conformations. η-θ are described as the dihedrals
between atoms C4'(i-1)-P(i)-C4'(i)-P(i+1) and P(i)-C4'(i)-P(i+1)-C4'(i+1)
respectively, where "i" represents residue number. So, essentially what I'm
trying to do via the CPPTRAJ multidihedral command is to find these
pseudo-torsions for each residue (nucleobase) in my tRNA, and I'm trying to
use the "offset" clause so some of the atoms in my custom
dihedral descriptions are being picked from prior and future residues (per
the η-θ definitions). Below is the bottom script I've been using to no
avail:
*parm stripped_unmod.prmtoptrajin aligned_unmod.nc
<http://aligned_unmod.nc>multidihedral resrange 1-76 dihtype
eta:C4':P:C4':P[:-1:1] #setup eta dihe, pick <a0> from prior
residue and <a3> from next residuemultidihedral resrange 1-76 dihtype
theta:P:C4':P:C4'[:2] #setup theta dihe, pick <a2> and <a3> from
next residuerunmultihist MDIH_00001[eta]:1-76 out dihedraleta.hist min -180
max 180 step 1 #Sort into histmultihist
MDIH_00002[theta]:1-76 out dihedraltheta.hist min -180 max 180 step 1
#Sort into histrun*
The common error message in my .out file is "Warning: No dihedrals selected
for topology stripped_unmod.prmtop", which I believe means that my custom
dihedral is not being recognized. I suspect it is an issue with my offset
clause being formatted incorrectly, however, I haven't been able to see any
examples of anyone using it so I don't know. I am naive for thinking that
this relatively complex dihedral measurement is something that can be done
with CPPTRAJ? Or is my input just wrong? Any help on this issue would be
greatly appreciated. Attached is a screenshot from the amber manual
detailing the multidihedral command and offset clause that seems to best
fit what I'm trying to accomplish here.
V. Best,
Kyle Warren
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