Hi,
Visualization software won't always draw a bond if the two atoms aren't in
some required distance, ie Pymol won't draw a bond if your atoms are 3 A
apart, so PDBs aren't the best way to check if the bond itself was formed.
You can check the prmtop file to see if the bond is present in with parmed,
though (I think leap can also do it?) with some input script like
ca >parmed.in<<EOF
parm name.prmtop
printBonds
go
EOF
parmed -i parmed.in -O > bonds.log
And just look up your atoms in the list to make sure they're bonded.
Best,
Kenneth
On Mon, Jan 11, 2021 at 4:38 PM Victoria E Hill <vehill1.sheffield.ac.uk>
wrote:
> Hi,
>
> I am trying to create two bonds in leap using the script:
>
> source leaprc.ff14SBcirc
> addAtomTypes {
> { "C1" "C" "sp2" }
> { "C2" "C" "sp2" }
> { "CI" "C" "sp3" }
> { "CE" "C" "sp3" }
> }
> loadoff parmBSC1.lib
> loadamberparams frcmod.parmbsc1
> addPdbAtomMap {{OP1 O1P}{OP2 O2P}{H5' H5'1}{H5'' H5'2}{H2' H2'1}{H2''
> H2'2}}
> set default PBradii mbondi3
>
> dna = loadpdb amber.339t30_newbond.pdb
>
> bond dna.1.P dna.339.O3'
> bond dna.340.P dna.678.O3'
>
> savepdb dna check.pdb
> saveamberparm dna 339t30.top 339t30.crd
>
> But when I check the output PDB file, no bond has been created.
>
> Could you please advise?
>
> Thanks,
> Victoria
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Received on Mon Jan 11 2021 - 14:30:01 PST
