Dear Jason
Thank you for your reply.
But I already made changes at both place in "mdread.f" file.
Then again recompiled AMBER11.
but still facing same problem of bad atom type FE.
Please suggest me what to do?
I am attaching edited "mdread.f" file. where i made changes. You can track
those changes by searching keyword "Prajwal" in this file.
Thank you
On Tue, Jan 8, 2013 at 8:54 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Thanks and Regards,
---------------------------------------------
Prajwal Nandekar
Ph. D. Scholar
Department of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research (NIPER)
Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
Mob. 09780741228*
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- application/octet-stream attachment: mdread.f
Received on Wed Jan 09 2013 - 06:30:04 PST
