How did you prepare your complex, receptor, and ligand topology files? For
this type of calculations you have to strip off the water molecules and
counter ions and just load the complex pdb file and prepare complex.top.
Then remove the ligand and prepare receptor.top. Finally load ligand.mol2
and make ligand.top. This should fix your problem.
mani
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.
>
> Regards
>
> Arunima
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Manikanthan Bhavaraju
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 18 2014 - 22:00:04 PDT
