Edit sander's mdread.f file ($AMBERHOME/src/sander/mdread.f) and look for
the phrase "bad atom type". It should occur twice -- once (commented out)
for the gbsa=1 code path and the second time (not commented out) for the
gbsa=2 code path. You'll need to provide a default radius here (like
what's done for gbsa=1) or at least provide one for Br to avoid seeing this
error message.
HTH,
Jason
On Fri, Nov 11, 2011 at 4:17 PM, Hector A. Baldoni <hbaldoni.unsl.edu.ar>wrote:
> Dear Amber users,
>
> progress.log: bad atom type: Br
>
> Is the error message I got trying to make GB and PB energy decomposition
> using MMPBSA.py.MPI with AT1.5. Can someone tell me how to fix it ?
>
> Best Regards,
> Hector.
>
> ---------------------------------
> Dr. Hector A. Baldoni
> Area de Quimica General e Inorganica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)2652-423789 ext. 157
> ----------------------------------
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 Fri Nov 11 2011 - 19:30:04 PST
