Dear Sir
>
> While executing the command for MMPBSA.py for protein-ligand interaction
>
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> com_solvated.top -cp com.top -rp 3pta.top -lp ZINC3781.top -y *.crd
> It showed the following error
>
>
> Number of atoms in Amber Restart 3pta.crd (14254) does not
> match number associated parmtop (194556)
>
As far as error messages from Amber go, this one is pretty straightforward.
> Could not set 3pta.crd for reading
> could not set up trajectory
>
> cpptraj failed when querying 3pta.crd
>
> I request you to kindly guide in debugging the error.
>
When you use the flag "-y *.crd", it tries to use every file that ends with
.crd as an input trajectory for MMPBSA.py. If you supply a solvated
topology file, then MMPBSA.py assumes that the input trajectories
correspond with that solvated topology file and needs to have its solvent
and ion residues stripped away in preparation for MM/PBSA analyses.
I suspect that 3pta.crd is a coordinate file that has only the coordinates
of the receptor (3pta.top), not the coordinates of the bound complex
immersed in solvent. As a result, it is incompatible with the solvated
topology file. Because it is a restart file, cpptraj helpfully identifies
the discrepancy between the number of atoms in the coordinate file (14,254)
and the number of atoms in the topology file it's trying to use to process
those coordinates (194,556).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
Dear Sir,
As per the tutorial instruction provided by Ross Walker,
I have stripped off the receptor and ligand from protein-ligand complex and
accordigly followed the tutorial to load receptor, ligand and complex.
Subsequently solvated the complex and went ahead with minimization and till
production step.
Here 3pta is the receptor and the protein-ligand complex is already
solvated and subsequently used for furthur evaluation.
I am not geting exactly how to resolve this error. I request you to kindly
guide me in debugging the error.
Regards
Arunima
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Received on Tue Mar 18 2014 - 21:30:04 PDT
