Re: [AMBER] MMPBSA.py calculations...bad atom type

From: RANAJIT SHINDE <science.ranajitshinde.gmail.com>
Date: Mon, 7 Jun 2010 10:19:37 +0530

Option mmpbsa=1, has run the calculations successfully. The problem was with
the gb calculations and pb alone was running without the error. Thank you
very much Jason and Bill for the help and time.

The warning I could I see in FINAL_RESULTS_MMPBSA.dat is this:



WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND, ANGLE,
AND/OR DIHED). CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY
NOT BE RELIABLE (check differences)!



I already have performed the both calculations with mm_pbsa.pl script with
250 snapshots. The energies of the obtained by both scripts are very much
similar [mm_pbsa.pl (gb/pb) (-64.49/ -61.96)] [MMPBSA.py (250 snapshots),
(gb/pb) (-64.62/ -59.37)].



I did not see any such warning while mm_pbsa.pl calculations. So how to make
sure that the results are reliable?



Regarding bad atom types (br), a statement is also seen in the
_MMPBSA_complex_gb.mdout. It reads as,



Using carbon SA parms for atom typebr



I looked into mdread.f file in /opt/amber10/src/sander. I could see the
statement “Using carbon SA parms for atom type” but not find the bromine
atom parameters. Could you specify the position to be modified?



I am attaching _MMPBSA_complex_gb.mdout and FINAL_RESULTS_MMPBSA.dat for
more information.



Thank you



Ranajit Shinde


On Sat, Jun 5, 2010 at 7:10 PM, Jason Swails <jason.swails.gmail.com> wrote:

> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Sun Jun 06 2010 - 22:00:03 PDT
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