[AMBER] DNA Strand Broken after minimization

From: Sumon Naskar <205030041.iitb.ac.in>
Date: Tue, 13 Jul 2021 15:52:44 +0530

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

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

Like here is no connection between the *P* atom and the O3' of


Sumon Naskar
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Received on Tue Jul 13 2021 - 03:30:02 PDT
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