On Tue, Jan 8, 2013 at 9:22 AM, Prajwal Nandekar
<prajwal.pharm07.gmail.com>wrote:
> Dear Amber Users,
>
> I have tried to run MM-GBSA calculations on CYP450 protein containing HEME
> using Python script (MMPBSA.py).
> I come-up with error message;
> -----------------------------------------------------
> 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.
>
> ------------------------------------------------------------------------------------------------------
>
> I am using Amber Tools1.5 with Amber11.
> I have tried to solve the error as mentioned in previous archives.
> http://archive.ambermd.org/201003/0002.html
> http://archive.ambermd.org/201201/0129.html
> http://archive.ambermd.org/201201/0131.html
>
> I have made necessary changes in files "*$AMBERHOME/src/sander/mdread.f"*
> and
> "*mm_pbsa_calceneent.pm" *(added ionic radii for FE atom)*.*
> Then I re-compiled Amber11 completely.
> But still I am facing same problem of Bad atom type FE.
> If anybody solved this problem for CYP450 system then please suggest me
> what to do?
>
mm_pbsa_calceneent.pm has nothing to do with MMPBSA.py. There are two
places in mdread.f that you need to add a radius for FE -- one is for the
'gbsa=1' method and the other is for the 'gbsa=2' method. I'm guessing you
only made the change in one place, correct? And you're probably using the
other surface area calculation method ;).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jan 08 2013 - 07:30:03 PST
