Hi
So I think what is going on here is that when I originally wrote
'multidihedral' I was interested in looking for canonical dihedrals,
so I built in a check that the 4 atoms in question were indeed
connected by bonds. Since you have pseudo-dihedrals here,
'multidihedral' is assuming it can't find the right atoms since they
aren't bonded.
HOWEVER, you can get around this by using a simple for loop. Here is
one I just came up with and (very briefly) tested:
parm stripped_unmod.prmtop
trajin aligned_unmod.nc
# Loop over residues
# j will be "middle", i is previous, k is next
for j=2;j<75;j++
i = $j - 1
k = $j + 1
# This will convert the loop variables into mask expressions
set ires = :
set ires += $i
set jres = :
set jres += $j
set kres = :
set kres += $k
# Calc the dihedrals
dihedral eta$j $ires.C4' $jres.P $jres.C4' $kres.P
dihedral theta$j $jres.P $jres.C4' $kres.P $kres.C4'
done
run
This *should* work, but please do test it on a small number of frames
(10-100) and make sure it's giving you what you want.
Hope this helps,
-Dan
On Fri, Aug 16, 2024 at 10:53 AM Warren, Kyle Benjamin via AMBER
<amber.ambermd.org> wrote:
>
> 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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> AMBER.ambermd.org
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Received on Fri Aug 16 2024 - 13:00:01 PDT
