On Tue, Apr 19, 2011 at 7:34 PM, Gabriel Urquiza <urquizagabes.gmail.com>wrote:
> Dear amberists,
>
> I am having some problemas when I try to run MMPBSA.py on several short
> dynamics. My system is an explicitly solvated protein with a
> ligand, sodium ions and a flavin residue (which has been parametrized using
> antechamber and parmchk).
>
> I run it with this input:
>
> &general
> startframe=1,
> endframe=1000000,
> interval=50,
> verbose=2,
> keep_files=1,
> strip_mask=":WAT:Na+",
>
You should leave this at its default value, unless you want to keep any ions
in there.
> ligand_mask=":O01",
>
If you don't specify both receptor_mask and ligand_mask, it will ignore this
and just use the default.
entropy=1,
> /
>
> &gb
> igb=5,
> saltcon=0.150,
> /
>
> &pb
> istrng=0.15, fillratio=4.0
> /
>
> The residue name is O01 because it is the first of a series of related
> compounds. I run MMPBSA.py and it gives me this:
>
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
>
This suggests that your prmtop files don't match the trajectory files that
are generated by MMPBSA.py.
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> Error: Sander output is missing values!
> VDWAALS = ************* EEL = -22412.2843 EGB =
> -3345.9563
>
This all but confirms it. Try visualizing _MMPBSA_complex.mdcrd with your
complex prmtop, _MMPBSA_receptor.mdcrd with your receptor prmtop, and
_MMPBSA_ligand.mdcrd with your ligand prmtop. If the structures look
warped, then something is messed up and you have to fix your prmtops (or
just use the default strip_mask).
HTH,
Jason
>
> ptraj found! Using /opt/amber11/exe/ptraj
> sander found! Using /opt/amber11/exe/sander (serial only!)
>
> Preparing trajectories with ptraj...
> Beginning quasi-harmonic entropy calculation with ptraj...
> 70 frames were read in and processed by ptraj for use in calculation.
>
> Starting sander calls
>
> Starting gb calculation...
>
> Starting pb calculation...
>
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
>
> There are no values of GB or PB in the output. Something probably went
> wrong
> (no kidding?).
>
> I made PDB files for the minimization step and for several snapshots of the
> dynamics using ambpdb. I also checked THE dynamics
> themselves. All of that using VMD. The snapshots seemed fine as well as the
> trajectories. I also checked the topologies used by the
> MMPBSA.py and all of them were at the right place.
>
> I looked around the list for problems such as these but i didn't find one
> that matched the context I am facing right now. Also, my trajectories
> aren't compressed.
>
> Looking forward to hear your ideas.
>
> Gabriel
>
> -----
> Graduation student at Federal University of Paraíba, Brazil.
> LQQC - Laboratory of Computational Quantum Chemistry
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 19 2011 - 20:30:03 PDT
