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 Mon Dec 15 2025 - 06:00:03 PST
