Could you send me your topology files and a couple frames of your trajectory
so I can take a look?
Thanks!
Jason
On Fri, Sep 16, 2011 at 12:13 PM, Antje Wolf
<antje.wolf.scai.fraunhofer.de>wrote:
> DEar Jason,
>
> No, I generated all topology files in one leap step, so the scaling factors
> should be consistent across ligand/complex and receptor/complex. Any tip
> where I could have a look to find out what exactly is going on?
>
> Thanks,
> Antje
>
> ----- Ursprüngliche Mail -----
> | 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
> | _______________________________________________
> | 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 - 10:00:04 PDT
