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On Wed, 2014-02-19 at 09:31 -0300, ricardo.miranda.ifpa.edu.br wrote:
> Dear!
>
> I'm trying to run MMPBSA and is giving an error, you let me know how I
> can fix this error? My system has:
> ligand.top
> receptor.top
> complex.top
> complex_box.top (complex with sodium-Na + ions)
> The command to run is:
> MMPBSA.py-O-i-MM PBSA_NM.in
> FINAL_RESULTS_MMPBSA.dat-of-the-FINAL_DECOMP_MMPBSA.dat
> complex_box.top sp-cp-rp complex.top receptor.top-lp-y ligand.top
> prod5ns.mdcrd
There is no way this command would run as you've copied it here. Please
be careful to report exactly what you did, and make sure the formatting
of the commands and input you used is correct.
> and the error I'm having is this below:
> Loading and checking parameter files for compatibility ...
> PrmtopError: Topology files have inconsistent RADIUS_SETs
> Exiting. All files have been retained.
This is a fairly straightforward error message. The implicit solvation
methods used here (with the exception of 3D-RISM, I believe) requires
some definition of the 'solvation radii', which is effectively how 'big'
an atom is. It is used to construct the boundary between the internal
dielectric of the substance (1 to 2) and the external dielectric of the
solvent (~80 for water). PB and GB construct this dielectric boundary
differently, but both require the size of each atom as input. This
input is provided in the topology file (sections RADII and RADIUS_SET).
Since the solvation free energies calculated by these methods are
incredibly sensitive to the choice of the initial radii, you MUST use a
consistent set of radii for each topology file in order to get
reasonable answers. This was a check implemented in MMPBSA.py to
prevent you from making this mistake and not realizing it.
The solution is to go back and make a consistent set of topology files
using the suggested radii. You can either use the "set default PBRadii"
command in tleap when creating the topology files or you can run your
existing topology files through ParmEd and use the "changeRadii"
command. They are all described in the AmberTools manual. The
suggested radius set for each type of implicit solvent calculation is
shown in the AmberTools manual for PB and in the Amber manual for GB
(under the description of the igb variable).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 19 2014 - 05:00:02 PST
