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
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Received on Fri Sep 16 2011 - 09:30:03 PDT
