On Wed, Mar 19, 2014 at 12:06 AM, 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
>
>
> 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.
>
Read my answer more carefully. You only want to specify the trajectories
from the simulation with the "-y" flag, NOT the restart files generated for
the unsolvated complex, receptor, and ligand.
It also helps to understand the basics of invoking programs from the
command-line using a shell and the semantics of wildcard expansion (i.e.,
what it means when you do "-y *.crd" and "-y prod?.crd").
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 19 2014 - 06:30:02 PDT
