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+",
ligand_mask=":O01",
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
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
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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Received on Tue Apr 19 2011 - 20:00:02 PDT
