On Mon, Mar 17, 2014 at 10:55 PM, Arunima Shilpi <writetoash28.gmail.com>wrote:
> 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
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Received on Tue Mar 18 2014 - 03:00:03 PDT
