Hi,
I am able to convert my files to to amber format using CHAMBER and got the paramtop and inpcrd files. Now, I want to perform MMPBSA calculations my system firstmolecule-dna. The files I have is solvated, complex, receptor and ligand, and the Production.dcd file that I got from NAMD simulations. The files generated by MMPBSA of _MMPBSA_complex.pdb, _MMPBSA_repetor.pdb, _MMPBSA_ligand.pdb having change in box size, the ions with dna moved away from firstmolecule, but, when I had checked the trajectory in VMD the MD looks correct.
I am using Ambertool 14 and Amber 14
I had modified my files as instructed here (
http://archive.ambermd.org/201303/0409.html) and my mdins files are as follows:
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o out.dat -sp solvated.prmtop -cp complex.prmtop -rp firstmolecule.prmtop -lp dna.prmtop -y ../Production.dcd -make-mdins
_MMPBSA_gb.mdin
File generated by MMPBSA.py
&cntrl
nsnb=99999, dec_verbose=0, ntb=0,
surften=0.0072, extdiel=80.0, ncyc=0,
cut=999.0, saltcon=0.1, imin=5, igb=2,
/
_MMPBSA_pb.mdin
File generated by MMPBSA.py
&cntrl
nsnb=99999, ipb=2,
ntb=0, cut=999.0, imin=5, igb=10,
/
&pb
use_sav=0, sprob=1.4, dprob=1.4, inp=2,
npbopt=1, eneopt=1, bcopt=5,
npbverb=1, accept=0.000001,
istrng=100.0, maxitn=1000,
fillratio=4.0, radiopt=0,
/
I had modified the mmpbsa.in files too by adding use_sander=1 in &genral as follows:
Input file for running PB and GB
&general
endframe=10000, verbose=1, use_sander=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
Finally, I got this error again and again, the "_MMPBSA_complex_gb.mdout.0" file is attached.
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o out.dat -sp solvated.prmtop -cp complex.prmtop -rp firstmolecule.prmtop -lp dna.prmtop -y ../Production.dcd -use-mdins
Loading and checking parameter files for compatibility...
CHAMBER prmtops found. Forcing use of sander
sander found! Using /home/cbme/amber14/bin/sander
cpptraj found! Using /home/cbme/amber14/bin/cpptraj
Preparing trajectories for simulation...
10000 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /home/cbme/amber14/bin/sander
calculating complex contribution...
File "/home/cbme/amber14/bin/MMPBSA.py", line 96, in <module>
app.run_mmpbsa()
File "/home/cbme/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/cbme/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/cbme/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
self.prmtop))
CalcError: /home/cbme/amber14/bin/sander failed with prmtop complex.prmtop!
Exiting. All files have been retained.
I dont understand where is the problem?, can anyone help me to solve this problem ?
What should I do to make it running??
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Received on Wed Dec 10 2014 - 19:30:02 PST
