Date: Tue, 13 Jul 2021 23:58:55 +0530
I'm sure no bond is present between the P-atom and the O3'. The usual
bond length between P and the O3' atoms is around 1.6 Angstrom but in my
structure where the DNA strand is terminated, the distance between the
P-atom and the O3' atom is 3.9 Angstrom. Here are the snapshots from the
PYMOL visualization software.
On 2021-07-13 22:43, Carlos Simmerling wrote:
> 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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