I’m dealing with a complex consisting of two protein chains (125 residues each) and two ligands. I was able to calculate DeltaG of the complex.
parminfo for the complex is:
> parminfo
Topology complex_solv.prmtop contains 42239 atoms.
I want to evaluate DeltaG of the two protein chains without the two ligands (named DE3, DE4). I’ve used ante-mmpbsa.py to generate new topologies for the unliganded complex.
ante-mmpbsa.py -p complex_solv.prmtop -s :DE3,:DE4,:WAT,Na+ -c complex.prmtop -r chainA.prmtop -m :1-125 -l chainB.prmtop --radii=mbondi2
New complex(ChainA+ChainB)
parminfo
Topology complex.prmtop contains 3984 atoms.
Title: default_name
250 residues.
For mmgbsa.py, I used the following input script:
Input file for running PB and GB
&general
strip_mask = :DE3,:DE4,:WAT,Na+
endframe=10000, verbose=1, interval=10,
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&decomp
idecomp=1,
dec_verbose=1,
/
When I run
mpirun -np 4 MMPBSA.py.MPI -O -i decomp.in -o FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP__MMPBSA.dat -sp complex_solv.prmtop -cp complex.prmtop -rp chainA.prmtop -lp chainB.prmtop -y *.nc
I get the following error.
AmberParmError: FLAG ATOMIC_NUMBER has 42239 elements; expected 3984
Error occured on rank 2.
Exiting. All files have been retained.
AmberParmError: FLAG ATOMIC_NUMBER has 42239 elements; expected 3984
Error occured on rank 3.
I’m rather perplexed because the mmpbsa input script has the same strip mask as ante-mmpbsa.py.
Any suggestions would be most helpful
Regards
George
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Received on Mon Aug 10 2015 - 10:00:02 PDT
