Re: [AMBER] MM/PBSA (Problem in snapshot generation)

From: Dwight McGee <>
Date: Mon, 21 Mar 2011 13:43:56 -0400


 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. How did you arrive at the conclusion that the
snapshots were made incorrectly (did an error occur when trying to calculate
the binding affinity)? One error could be that you are not using the correct
topology file with the .crd generated by when viewing the
structure in for example VMD/Pymol or etc. 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?

On Mon, Mar 21, 2011 at 1:00 PM, mish <> 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:
> NTOTAL 37807 # total no of atoms (including water and
> Ions) in traj file
> #
> LSTART 3923 # Beginning of Ligand one (26 atoms only)
> LSTOP 3948 # end of ligand one
> 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

T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
"Problems cannot be solved at the same level of awareness that created
                Albert Einstein
AMBER mailing list
Received on Mon Mar 21 2011 - 11:00:04 PDT
Custom Search