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
>
> _______________________________________________
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> 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
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Received on Sat Jun 05 2010 - 04:30:03 PDT
