On Mon, Mar 21, 2011 at 6:43 PM, Dwight McGee <dwight.mcgee.gmail.com>wrote:
> Hi,
>
> Please correct me if I wrong here but the way I have understood what you
> are trying to do is calculate the binding of two different ligands when the
> other is bound to the complex.
Yes, this is the way I am trying to compute the energy of one ligand.
> How did you arrive at the conclusion that the
> snapshots were made incorrectly (did an error occur when trying to
> calculate
> the binding affinity)?
There was no error during the run but when I visualize the generated .crd
with corresponding prm file, ligands are distorted.
> One error could be that you are not using the correct
> topology file with the .crd generated by mmpbsa.pl when viewing the
> structure in for example VMD/Pymol or etc.
I generated a pdb file from the simulation of the complex. Now, all the
water molecule were deleted. five files (complex, receptor+lig2, rec+lig1,
lig1, lig2) were save separately, and these PDB were used to generate prm
files. I used same the ff which I used in running simulation.
> Check the crd file generated to
> see if got the total number of atoms correct at least? Did you make 5
> topology files: *1)* complex, *2)* receptor with ligand-2 bound
> *3)*ligand-1 only
> *4)* receptor with ligand-1 bound *5)* ligand-2 only?
> Yes I did the same. and atom numbers are correct perfectly alright.
>
> On Mon, Mar 21, 2011 at 1:00 PM, mish <smncbr.gmail.com> wrote:
>
> > Hi
> >
> > I am facing a problem in MM/PBSa calculation. Now, I am using perl scrip
> in
> > amber 11.0 and the problem is in snapshot generation. The snapshots have
> > very weird structure of the ligand. I have checked all the parm files
> > (complex, protein, ligand) and atom numbers in input scripts and
> everything
> > seems right. I had MD with 2 ligands and trying to compute the binding
> > energy one by one, when second some will be part of receptor.
> >
> > . Marked section is like:
> >
> > BOX YES
> > NTOTAL 37807 # total no of atoms (including water and
> > Ions) in traj file
> > #
> > NUMBER_LIG_GROUPS 1
> > LSTART 3923 # Beginning of Ligand one (26 atoms only)
> > LSTOP 3948 # end of ligand one
> > NUMBER_REC_GROUPS 2
> > RSTART 1
> > RSTOP 3922 # end of receptor
> > RSTART 3949 # beginning of ligand 2, which is a part
> of
> > receptor (26*5 atoms)
> > RSTOP 4078 # end of ligand 2
> >
> >
> > What could be the way to debut the problem ? why the ligands (both lig-1
> > and
> > lig-2 ) are are getting wrong connectivity in snapshots of complex.
> > receptor
> > as well as ligand ? am I doing some blunder mistake ?
> >
> > Sincerely
> > mish
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
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Received on Mon Mar 21 2011 - 11:30:03 PDT
