Problems Building Circular DNA

From: Sebastian S (thecromicusproductions_at_gmail.com)
Date: Mon Jan 11 2021 - 19:42:36 CST

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Hi everyone,

I'm trying to simulate a circular DNA molecule. To do this, I apply the
patch seen below but when I run the simulation I get the following error
message:

FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR ON5 P (ATOMS 2304 2271)
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR ON5 P (ATOMS 2304
2271)

This error does not happen for regular DNA, so I think I'm doing something
wrong with the patch. I've been trying different things but nothing seems
to work. Any help would be appreciated!

Thanks,

Sebastian

Code to apply the patch (the dsDNA was built with nab and has 70
base-pairss)

resetpsf
mol load pdb DNA.pdb
set newfile DNA_psfgen
set TOPOFILE ./top_all36_na.inp
pdbalias residue DT THY
pdbalias residue DG GUA
pdbalias residue DC CYT
pdbalias residue DA ADE
proc psfalias {} {
        # Define common aliases
        # Here's for nucleics
        pdbalias residue G GUA
        pdbalias residue C CYT
        pdbalias residue A ADE
        pdbalias residue T THY
        foreach bp { GUA CYT ADE THY URA } {
                pdbalias atom $bp "O5\*" O5'
                pdbalias atom $bp "C5\*" C5'
                pdbalias atom $bp "O4\*" O4'
                pdbalias atom $bp "C4\*" C4'
                pdbalias atom $bp "C3\*" C3'
                pdbalias atom $bp "O3\*" O3'
                pdbalias atom $bp "C2\*" C2'
                pdbalias atom $bp "O2\*" O2'
                pdbalias atom $bp "C1\*" C1'
        }
     }
package require psfgen
topology $TOPOFILE
psfalias
set sel [atomselect top "chain A"]
set listA [lsort -unique [$sel get {resid resname}] ]
foreach selatom $sel {
$selatom set segid ADNA
}
$sel writepdb ADNA.pdb
set sel [atomselect top "chain B"]
set listB [lsort -unique [$sel get {resid resname}] ]
foreach selatom $sel {
$selatom set segid BDNA
}
$sel writepdb BDNA.pdb
# splitting the input pdb
set segidList {ADNA BDNA}
set patchList [list $listA $listB]
segment ADNA {
     first 5TER
     last 3TER
     pdb ADNA.pdb
}
segment BDNA {
     first 5TER
     last 3TER
     pdb BDNA.pdb
}

puts "Begin to patch to make DEOXYribose"
  # patch to make DEOXYribose
  # purine use patch DEO2
  # pyrimidine use patch DEO1

foreach segid $segidList tmpList $patchList {
puts "segid: $segid tmpList:$tmpList"
     foreach record $tmpList {
        foreach {resid resname} $record { break }
        if {$resname == "THY" || $resname == "CYT" } {
            patch DEO1 ${segid}:$resid
            puts "patch DEO1 ${segid}:$resid"
        }
        if {$resname == "ADE" || $resname == "GUA" } {
            puts "patch DEO2 ${segid}:$resid"
            patch DEO2 ${segid}:$resid
        }
     }
     coordpdb ${segid}.pdb
}

puts "End of DEOXYribose "
guesscoord
patch CY35 ADNA:70
patch CY35 BDNA:70
patch LKNA ADNA:1 ADNA:70
patch LKNA BDNA:1 BDNA:70
regenerate angles dihedrals
writepsf $newfile.psf
writepdb $newfile.pdb

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