Deal all,
I have been trying to run MMPBSA/GBSA analysis based on the Advanced Amber
tutorial posted in the Amber site. I first ran the tutorial using the same
ras-raf protein complex provided in the tutorial and it ran without any
problem.
The problem came when I wanted run my own system (Protein protein complex).
Even though I used exact same input files and command (except changing
residue numbers) I am getting some error messages as follows:
................................................................................................................................................
* mmpbsa.in <
http://mmpbsa.in>*
Input file for running PB and GB
&general
endframe=50, verbose=1,
# entropy=1,
/
&gb
igb=8, saltcon=0.100
/
&pb
inp=1,radiopt=0,istrng=0.100,
/
~
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
A_B_solvated.prmtop -cp A_B-clean.prmtop -rp A-clean.prmtop -lp
B-clean.prmtop -y *.mdcrd.gz
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using
/opt/software/Amber/14update--Intel-13.0.1.117/bin/mmpbsa_py_energy
cpptraj found! Using
/opt/software/Amber/14update--Intel-13.0.1.117/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with
/opt/software/Amber/14update--Intel-13.0.1.117/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
File "/opt/software/Amber/14update--Intel-13.0.1.117/bin/MMPBSA.py", line
96, in <module>
app.run_mmpbsa()
File
"/opt/software/Amber/14update--Intel-13.0.1.117/bin/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/opt/software/Amber/14update--Intel-13.0.1.117/bin/MMPBSA_mods/calculation.py",
line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/opt/software/Amber/14update--Intel-13.0.1.117/bin/MMPBSA_mods/calculation.py",
line 459, in run
self.prmtop))
CalcError: /opt/software/Amber/14update--Intel-13.0.1.117/bin/*cpptraj
failed with prmtop A-clean.prmtop!*
Exiting. All files have been retained.
.............................................................................................................................................
Simulation and production phases run fine without any problem. But when I
run the mmpbsa.in command (as above), I get this message saying that one of
my topology files is the problem. If I switch protein A to ligand protein
(lp) and protein B to receptor protein (rp) then the system goes one more
step to "calculating ligand contribution" and I will get the same error
message. So it is clear that the system is pointing out some kind of
problem with my A-clean.prmtop file but I have no idea
i) why that problem is arising
ii) how to verify where the problem is??
Another thing is, if I remove GB command in mmpbsa.in input file, PBSA runs
fine and also give me the final free energy. So it looks like GB is the
problem. But it looks weird to me that PB runs fine despite having error
with one of the topology files because PB uses that topology files as well.
I tried another system and I am getting similar error message. So I am
assuming I am not preparing this individual PDB files properly. Is there
anything in particular I am missing here???
The way I prepared the individual A and B proteins from the complex is:
I have complex crystal structure. Then I use Pdb4amber command to clean and
dry (hydrogens and water). Then I save that as PDB. I open that PDB in
PyMol and delete sequences for B and save as A and vice versa. Then I run
tleap to save all teh parameters. Am I doing something wrong here?? Does
any body have better way to prepare separate PDB from complex???
So I am very confused on whats going on and how to approach this problem. I
tried to follow few other posts from past in Amber mailing list but still
didn't help me that much.
I would be very grateful for you input on this issue.
Jag
Graduate Student, Chemistry, MSU
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Received on Wed Feb 10 2016 - 07:00:05 PST
