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 - 03:30:02 PDT
