On Fri, Sep 16, 2011 at 2:51 AM, Antje Wolf
<antje.wolf.scai.fraunhofer.de>wrote:
> I am combining different force fields for the system I am studying:
> parm99SB+bsc0 for the receptor and a tailored ff for the ligand that is
> using different 1-4 scaling factors (SCEE=1.0 and SCNB=1.0). I was very
> careful about setting it up and used the most recent version of tleap to
> have the different values for SCEE and SCNB written into the topology files.
>
This would certainly cause the behavior if the 1-4 scaling factors for the
ligand atoms is different in the complex and the ligand topology files. If
the FF for the ligand treated in the complex is different than the FF for
the isolated ligand, then you're going to have a problem (likewise if the FF
for the receptor atoms in the complex is different than the FF for the
isolated receptor).
Is this the case?
--Jason
> Could this be the source for the large difference in the calculation?
>
> Anybody experienced a similar behavior?
>
> Antje
>
> ----- Ursprüngliche Mail -----
> | On Thu, Sep 15, 2011 at 11:34 AM, Antje Wolf
> | <antje.wolf.scai.fraunhofer.de>wrote:
> |
> | > The differences in the FINAL_RESULTS_MMPBSA.dat are:
> | >
> | > Energy Component Average Std. Dev. Std.
> | > Err. of
> | > Mean
> | >
> | >
> -------------------------------------------------------------------------------
> | > 1-4 VDW -2.2416 0.5667
> | > 0.0567
> | > 1-4 EEL -1.4070 0.0306
> | > 0.0031
> | >
> |
> | Yea, I would say that is an unacceptable difference. I've never seen
> | this
> | behavior before... If this is a bug, though, it's a bug in sander
> | since all
> | MMPBSA.py does is parse the sander output
> |
> |
> | >
> | > But the final deltaG differs by 6 kcal/mol depending on if I
> | > include
> | > &decomp or not. That is quite a lot.
> | >
> | > Antje
> | >
> | > ----- Ursprüngliche Mail -----
> | > | Look at your FINAL_RESULTS output file (*not* the decomp). It
> | > | should
> | > | print
> | > | out the differences in the 1-4 VDW/EEL terms. If they are close
> | > | to
> | > | zero,
> | > | you should be fine.
> | > |
> | > | How large are those values?
> | > |
> | > | On Thu, Sep 15, 2011 at 8:13 AM, Antje Wolf
> | > | <antje.wolf.scai.fraunhofer.de>wrote:
> | > |
> | > | > Dear list,
> | > | >
> | > | > I am currently doing MM-PBSA calculations using the MMPBSA.py
> | > | > script
> | > | > (AmberTools1.5, AMBER11 with all latest bug fixes applied).
> | > | > What
> | > | > bothers me
> | > | > is a warning message when I include energy decomposition
> | > | > analysis.
> | > | > For both,
> | > | > Generalized Born and Poisson-Boltzmann, the final result file
> | > | > contains:
> | > | >
> | > | > WARNING: INCONSISTENCIES EXIST WITHIN 1-4 NON-BONDED TERMS.
> | > | > CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT
> | > | > BE
> | > | > RELIABLE
> | > | > (check differences)!
> | > | >
> | > | > Here is my mmpbsa.in file:
> | > | >
> | > | > &general
> | > | > endframe=100, verbose=1
> | > | > /
> | > | > &gb
> | > | > igb=2, saltcon=0.100
> | > | > /
> | > | > &pb
> | > | > istrng=0.100,
> | > | > /
> | > | > &decomp
> | > | > idecomp=1, dec_verbose=1,
> | > | > print_res="1-217"
> | > | > /
> | > | >
> | > | > When I do NOT include the &decomp namelist, no warning is
> | > | > printed
> | > | > and also
> | > | > my final deltaG values are different.
> | > | > Can I trust the energy decomposition results? Should I maybe
> | > | > try a
> | > | > different idecomp model?
> | > | >
> | > | > Thanks,
> | > | > Antje
> | > | >
> | > | > --
> | > | > Antje Wolf
> | > | >
> | > | > Fraunhofer-Institute for Algorithms and Scientific Computing
> | > | > (SCAI)
> | > | > Department Bioinformatics
> | > | > Schloss Birlinghoven
> | > | > D-53754 Sankt Augustin
> | > | >
> | > | > Tel.: +49 2241 14 2552
> | > | > E-mail: antje.wolf.scai.fraunhofer.de
> | > | > Internet: http://www.scai.fraunhofer.de
> | > | >
> | > | > _______________________________________________
> | > | > AMBER mailing list
> | > | > AMBER.ambermd.org
> | > | > http://lists.ambermd.org/mailman/listinfo/amber
> | > | >
> | > |
> | > |
> | > |
> | > | --
> | > | 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
> | > |
> | >
> | > --
> | > Antje Wolf
> | >
> | > Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
> | > Department Bioinformatics
> | > Schloss Birlinghoven
> | > D-53754 Sankt Augustin
> | >
> | > Tel.: +49 2241 14 2552
> | > E-mail: antje.wolf.scai.fraunhofer.de
> | > Internet: http://www.scai.fraunhofer.de
> | >
> | >
> | > _______________________________________________
> | > AMBER mailing list
> | > AMBER.ambermd.org
> | > http://lists.ambermd.org/mailman/listinfo/amber
> | >
> |
> |
> |
> | --
> | 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
> |
>
> --
> Antje Wolf
>
> Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
> Department Bioinformatics
> Schloss Birlinghoven
> D-53754 Sankt Augustin
>
> Tel.: +49 2241 14 2552
> E-mail: antje.wolf.scai.fraunhofer.de
> Internet: http://www.scai.fraunhofer.de
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Sep 16 2011 - 07:30:03 PDT
