Kindly suggest some ways to rectify this.
On 2025-12-15 19:29, Priyasha Majee wrote:
> Hello All,
>
> I am trying to do MMPBSA. My system is a complex of protein and DNA
> system with an incoming nucleotide. I want to see the binding affinity
> of nucleotide with DNA template in wild type and mutant protein-DNA
> system. My system has 1-347 amino acids, 348-349 ions and 350-377 DNA
> (both template and complementary ssDNA) and 378 as the incoming
> nucleotide. The system parameter file is nowation.prmtop which doesn't
> have water and Na+ ions. The corresponding trajectory is comp.nc. I
> tried to generate the complex, receptor and ligand .prmtop file using
> parmed. For complex I used:
>
> cp nowation.prmtop complex.prmtop
>
> For ligand
>
> Parmed nowation.prmtop
>
> Strip ! (:378)
>
> Outparm ligand.prmtop
>
> For Receptor
>
> Parmed nowation.prmtop
>
> Strip :'348-349, 378'
>
> Outparm receptor.prmtop
>
> The trajectory I am using the original trajectory stripped off water
> and ions.
>
> When I am trying to run the MMPBSA job,
>
> It is showing complex.prmtom != receptor.prmtop + ligand.prmtop.
>
> Kindly please suggest where am I going wrong?
>
> Thank you
>
> Regards
>
> Priyasha
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Received on Thu Dec 18 2025 - 01:00:03 PST
