Hi,
Without looking at your files directly it is difficult to say what else
could be happening. I would suggest possibly trying the MMPBSA python
version instead to see if you have better luck.
On Mon, Mar 21, 2011 at 2:06 PM, mish <smncbr.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
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 - 12:30:05 PDT
