Hello,
It appears as though this error only occurred for GB. You may want to
consider running the PB calculation only.
Another thing to try: specify gbsa=1 in the &gb namelist. I believe there
is no fatal error message associated with this option (it is commented out
in amber11, but I don't have a copy of amber10 to readily compare).
You can use the -rewrite-output option to write the output file just for
your PB results from the calculation you already did by making the followng
changes: remove the whole &gb namelist from your input file. Re-run the
same exact command you ran to run the calculation, but add -rewrite-output
at the end. This will just print your PB results to your output file.
Changing gbsa to 1 in your &gb section should fix it (though the surface
area for your bromine atom may not be properly calculated, but for a single
atom this is probably a small error). You could also find a radius to use
for Bromine atom types and add that radius to mdread.f and recompile sander.
Good luck!
Jason
On Sat, Jun 5, 2010 at 7:04 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> These two errors are related. You are getting no potential terms in your
> mdout files because there is a bad atom type and thus sander cannot
> calculate the potential energy terms for the system. MMPBSA.py does not
> define its own atom types the way that mm_pbsa.pl does, and thus changing
> atom types in mm_pbsa_calceneent.pm won't change anything for MMPBSA.py.
> MMPBSA.py uses the same atom type list that sander does. Have you taken a
> look at the PB and GB mdout files to see if there are any error messages in
> there? I wouldn't think that you should be having a bad atom type since I
> assume you ran the simulation using sander, which has the same atom type
> definitions as MMPBSA.py. This error message, though, is really a sander
> error message, and needs to be fixed as such. Hopefully someone with more
> experience with bad atom types in sander can help out here.
>
> Good luck!
>
> -Bill
>
>
> On Sat, Jun 5, 2010 at 1:45 AM, RANAJIT SHINDE <
> science.ranajitshinde.gmail.com> wrote:
>
> > Dear all,
> >
> > We have amber10 and MMPBSA.py installed on CentOS. I am running mmpbsa
> > calculations for the enzyme-inhibitor complex where inhibitor has the
> > “bromine” atoms. After running the following command,
> >
> > $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> > complex_sol.prmtop -cp complex_vac.prmtop -rp protein.prmtop -lp
> > ligand.prmtop -y *.mdcrd
> >
> >
> >
> > calculations proceeded as this,
> >
> >
> >
> > ptraj found! Using /opt/amber10/bin/ptraj
> >
> > sander found! Using /opt/amber10/bin/sander
> >
> > Assuming /opt/amber10/bin/sander is part of
> >
> > amber9 or amber10. Using old PB input file.
> >
> > Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
> modified
> > Bondi radii (mbondi)
> >
> >
> >
> > Preparing trajectories with ptraj...
> >
> > 5 frames were read in and processed by ptraj for use in calculation.
> >
> >
> >
> > Starting calculations...
> >
> >
> >
> > Starting gb calculation...
> >
> >
> >
> > calculating ligand contribution...
> >
> > bad atom type: br
> >
> > calculating receptor contribution...
> >
> > calculating complex contribution...
> >
> > bad atom type: br
> >
> > Starting pb calculation...
> >
> >
> >
> > calculating ligand contribution...
> >
> > calculating receptor contribution...
> >
> > calculating complex contribution...
> >
> >
> >
> > Calculations complete. Writing output file(s)...
> >
> >
> >
> > Error: No potential terms in sander output! Check output files.
> >
> > NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> > --clean to erase these files.
> >
> >
> >
> > It encountered two problems. 1. bad atom type br and 2. Potential term.
> >
> > So could you please tell how to fix the bad atom type? Is there any file
> > which can be modified with atom types (like mm_pbsa_calceneent.pm in
> case
> > of
> > mm_pbsa.pl)?
> >
> > Is the problem of halogen atoms for mmpbsa calculation is taken care in
> > amber11?
> >
> > How to fix the error “no potential terms in sander output”?
> >
> > I am attaching FINAL_RESULTS_MMPBSA.dat file for the information.
> >
> > Kindly assist
> >
> > Ranajit Shinde
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jun 05 2010 - 07:00:04 PDT
