Then GBSA is set to 2 by default (decomp requires gbsa=2). This has been
addressed on the list before (you can probably google for it).
The solution is to add a default radius or the "real" radius to
$AMBERHOME/src/sander/mdread.f (look for the error message you're getting
-- that will take you to the relevant part of the code). Once you add code
to handle that atom, recompile sander and it should work.
HTH,
Jason
On Tue, Feb 28, 2012 at 7:08 PM, Osman, Roman <roman.osman.mssm.edu> wrote:
> Hi Dwight,
> No, gbsa=2 is not set, but, yes, I am doing energy decomposition.
> Here is the input file:
> Input file for running GB
> &general
> verbose=2, strip_mdcrd=1, strip_mask=":WAT",
> entropy=0, startframe=62, endframe=10000, interval=62
> /
> &decomp
> idecomp=2, dec_verbose=3,
> /
> &gb
> igb=5, saltcon=0.150
> /
> &pb
> istrng=0.150
> /
> &nmode
> nmstartframe=8, nmendframe=160, nminterval=6,
> maxcyc=50000, drms=0.0001, nmode_igb=1, nmode_istrng=0.1,
> /
>
> Thanks for your help.
> Rami
>
> On Feb 28, 2012, at 6:33 PM, Dwight McGee wrote:
>
> > Hi,
> >
> > Is gbsa=2 in your input? Are performing an energy decomposition
> analysis?
> >
> > On Tue, Feb 28, 2012 at 5:59 PM, Osman, Roman <roman.osman.mssm.edu>
> wrote:
> >
> >> Greetings,
> >>
> >> I am running an mmpbsa_py on a complex with a small molecule that
> contains
> >> Br.
> >> I am getting this error:
> >>
> >> Beginning GB calculations with sander...
> >> calculating complex contribution...
> >> bad atom type: br
> >>
> >> I assume the error is because of the Br.
> >> I would be grateful if you suggest how to fix this problem.
> >> Thanks very much,
> >>
> >> Roman Osman
> >>
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > T. Dwight McGee Jr.
> > Quantum Theory Project
> > University of Florida
> > Graduate Student
> > dwight.mcgee.gmail.com
> >
> > "Problems cannot be solved at the same level of awareness that created
> > them."
> > Albert Einstein
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 28 2012 - 18:00:02 PST
