Am 15.12.25 um 14:59 schrieb Priyasha Majee via AMBER:
>
>
> 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?
>
If I understand correctly then your procedure yields one prmtop-file for
the single nucleotide (ligand), one for the protein and DNA (receptor),
and one for the complex (protein, DNA, and two ions) - and thus your
complex file still contains those two ions, while they are not present
in the receptor or ligand file. If you strip them from the complex file,
it should work, and also, if you do not strip them from the receptor
file - depending of which system you want to study.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
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Received on Tue Dec 16 2025 - 06:00:02 PST
