Huh. Have you tried checking the output prmtops from ante-MMPBSA itself?
Specifically the FLAG ATOMIC_NUMBER portion, since it seems like a
strip_mask issue here, but the error message might be saying that there
might've been a hiccup somewhere with the input prmtops if your old ones
are working fine.
Best,
Kenneth
On Mon, Aug 10, 2015 at 1:37 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Thank you Kenneth,
>
> Tried it. I’m afraid it doesn’t work. When I re-run mmpbsa.py on the
> original topology (Dimer + Ligands) it runs without a problem.
>
>
> > On 10 Aug 2015, at 20:23, Kenneth Huang <kennethneltharion.gmail.com>
> wrote:
> >
> > 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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> >>
> >
> >
> >
> > --
> > Ask yourselves, all of you, what power would hell have if those
> imprisoned
> > here could not dream of heaven?
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Received on Mon Aug 10 2015 - 12:00:02 PDT
