It would help if you told us what versions of MMPBSA.py and Amber you were
using. Note that if you are _not_ using AmberTools 13, the next suggestion
will be to upgrade to AmberTools 13 and try that, since many bugs have been
fixed since the earlier versions were released.
Another comment here: I don't think that the GB models implemented in Amber
have really considered iron in its parametrization process, so results from
such systems may be suspect...
HTH,
Jason
On Tue, Jul 30, 2013 at 6:19 AM, tianchuan1015 <tianchuan1015.gmail.com>wrote:
> Dear amber.
>
> I was doing MD using amber on protein ligand interaction with MMPBSA, the
> Fe atom is not recognized by MMPBSA when doing decomposition.
> I have re-installed amber and add the modified mdread.f in the attachment.
> But the errors are also as follows
>
>
> Beginning GB calculations with sander...
> calculating complex contribution...
> bad atom type: FE
> Error: sander error during GB calculations!
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
> bad atom type: FE
> bad atom type: FE
> bad atom type: FE
> bad atom type: FE
> Error: sander error during GB calculations!Error: sander error during GB
> calculations!
>
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.NOTE: All files have been retained for
> debugging purposes. Type MMPBSA.py --clean to erase these files.
>
> Error: sander error during GB calculations!
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
> Error: sander error during GB calculations!
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
> Exit code -5 signaled from bnode12
> Killing remote processes...MPI process terminated unexpectedly
> bad atom type: FE
> Error: sander error during GB calculations!
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
> bad atom type: FE
> Error: sander error during GB calculations!
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
> bad atom type: FE
> Error: sander error during GB calculations!
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
>
>
> Is there a solution to solve this?
>
> best regards
> tianchuan1015
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 30 2013 - 05:00:02 PDT
