I could be a little off here, but the problem might be-
strip_mask=:DE3:DE4:WAT:Na+
>
You can try the above to see if it's fixed the issue.
Best,
Kenneth
On Mon, Aug 10, 2015 at 12:49 PM, George Tzotzos <gtzotzos.me.com> wrote:
> 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 - 10:30:04 PDT
