That's very possible, since I don't think that particular error message is
usually associated with MMPBSA.
I meant are there the appropriate number of numbers present? The error
message says that it's finding more with a topology (complex?) than it
expects, so it sounds like it's missing out on removing the solvent from
that section. If it is, you should see noticeably more numbers compared to
a protein only topology, since you have all the extra water atoms adding
onto it. If so, you could try manually removing solvent and ions, though
it'd be a time consuming workaround that you already circumvented.
On Monday, August 10, 2015, George Tzotzos <gtzotzos.me.com
<javascript:_e(%7B%7D,'cvml',
'gtzotzos.me.com');>> wrote:
> Kenneth, many thanks once again
>
> I think the bug is with cpptraj v.15
>
> I switched back to cpptraj v.13.24 and it works fine.
>
> Concerning the FLAG ATOMIC_NUMBER portion, what exactly do you want me to
> check.
> All prmtop files contain
> %FLAG ATOMIC_NUMBER
> %FORMAT(10I8)
>
> Regards
>
> George
>
> > On 10 Aug 2015, at 21:43, Kenneth Huang <kennethneltharion.gmail.com>
> wrote:
> >
> > 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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> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Ask yourselves, all of you, what power would hell have if those
> >> imprisoned
> >>> here could not dream of heaven?
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> >
> >
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> imprisoned
> > here could not dream of heaven?
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Received on Mon Aug 10 2015 - 13:00:03 PDT
