two things you might try:
1) pdb files don't always contain information about bonds, and programs use
distance between atoms to guess bonds. Your visualization software may be
doing this. If you use VMD, you can load the prmtop file first and then the
coordinates, and it will use bond info from the prmtop
2) use parmed on your prmtop and see if bonds are present using the
"printbonds" command.
On Tue, Jul 13, 2021 at 6:23 AM Sumon Naskar <205030041.iitb.ac.in> wrote:
> Dear sir,
>
> I was making a complex structure with the monomer of 5w2a for
> pre-insertion stage.
>
> First I removed the solvent molecules and the unwanted molecules. Then I
> removed the Magnesium atom and the incoming nucleotide from the pdb
> file.
>
> Then I load my adduct and the above mentioned pdb complex for making the
> required complex i.e complex with my adduct. By applying the below
> commands in leap.
>
> _source leaprc.protein.ff14SB_
>
> _source leaprc.DNA.bsc1_
>
> _source leaprc.water.tip3p_
>
> _U0 = loadmol2 ./CT-A_m1-c1_m2-c1.mol2_
>
> _frcmod1 = loadamberparams ./frcmod.known_
>
> _frcmod2 = loadamberparams ./frcmod.correspondence_
>
> _frcmod3 = loadamberparams ./output.frcmod_
>
> _complex = loadpdb complex.pdb_
>
> _check complex_
>
> _saveamberparm complex complex.prmtop complex.inpcrd_
>
> _ _
>
> Then I run a small minimization with this prmtop and inpcrd files to
> remove bad contacts. I got a ncrst file from here. I make a pdb file
> with the prmtop and this ncrst file. The pdb file I have get have one
> DNA strand terminated from the place where my adduct is attached.
>
> Can you please tell me why this is and happening? And how to fix this
> problem?
>
> Like here is no connection between the *P* atom and the O3' of
> guanosine.
>
> Regards,
>
> Sumon Naskar
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Received on Tue Jul 13 2021 - 10:30:03 PDT
