Hi George,
My mistake. -make-mdins and -use-mdins are command-line flags -- NOT
something that goes in the input file. I should have been clearer about
that.
On Thu, Aug 11, 2011 at 7:17 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Jason,
>
> Many thanks for this. Let me see if I understand the process you describe.
>
> 1. I need to run MMPBSA.py with an input file such as:
>
> Input file for running PB and GB
> &general
> "-make-mdins",
> endframe=50, verbose=1,
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
>
> Of course this doesn't work because -make-mdins is wrong. Can you please
> help with the syntax.
>
> 2. Assuming that all works, I should get a number of output files including
> _MMPBSA_pb.mdin. This I have to modify by including set npbopt=1.
>
You should only see temporary input files created, that is _MMPBSA_gb.mdin
and _MMPBSA_pb.mdin (and maybe one or 2 others).
>
> 3. Re-run MMPBSA.py using the same input file as in step 1 with the
> modification that instead of -make-mdins, I use -use-mdins.
>
On the command-line.
>
> 4. Repeat step 3 above with different saltcon values.
>
> Is this process what you suggested?
>
If you want to compare different salt concentrations or ionic strengths.
>
> I also have a general questions. Forgive my ignorance as I am a novice.
> What is the difference between PBSA in AmberTools and MMPBSA.py?
>
PBSA is the program written to actually solve the PB equation. MMPBSA.py is
more or less of a glorified bookkeeper and organizer. It arranges all of
the input files and data, sets up calculations, and calls different programs
(one of them being PBSA for solving the PB equation) to actually run the
calculation, then parses the output files at the end and calculates basic
statistics of the resulting data.
HTH,
Jason
>
> Your help is greatly appreciated
>
> George
>
>
> On Aug 11, 2011, at 5:13 AM, Jason Swails wrote:
>
> > On Wed, Aug 10, 2011 at 7:10 PM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> Jason,
> >>
> >> Thank you. Due to oversight I did not attach the script. I'm copying it
> >> below for easy reference. Is there something more that I should do under
> >> &pb? Can I use saltcon=x.xxx under &pb as well?
> >>
> >
> > istrng is PB's version of saltcon (ionic strength vs. salt
> concentration).
> > If you want to use the non-linear PB equation, you will need to run
> MMPBSA
> > with the -make-mdins flag, modify the _MMPBSA_pb.mdin file to use the
> > non-linear equation (set npbopt=1), then re-run MMPBSA with the
> -use-mdins
> > flag to make sure it reads in your modifications. Note that you need
> every
> > command-line flag present for each MMPBSA command (the first to create
> the
> > input files and the second to use the modified ones).
> >
> > HTH,
> > Jason
> >
> >
> >> Thanks in advance
> >>
> >> George
> >>
> >> Input file for running PB and GB
> >> &general
> >> endframe=50, verbose=1,
> >> # entropy=1,
> >> /
> >> &gb
> >> igb=2, saltcon=0.100
> >> /
> >> &pb
> >> istrng=0.100,
> >> /
> >>
> >> On Aug 10, 2011, at 11:04 PM, Jason Swails wrote:
> >>
> >>> If you really want to analyze salt effects, you should use the
> nonlinear
> >> PB
> >>> equation rather than GB, as it provides a better approximation.
> >>>
> >>> HTH,
> >>> Jason
> >>>
> >>> On Wed, Aug 10, 2011 at 9:26 AM, George Tzotzos <gtzotzos.me.com>
> wrote:
> >>>
> >>>> I'm trying to analyse the effect of ionic strength on the Delta G of
> >>>> binding of a protein-ligand complex.
> >>>>
> >>>> I've been trying to do this by changing saltcon in the script below
> from
> >>>> 0.1 through to 0.8. I've observed little or no difference which does
> >> not
> >>>> much experimental data.
> >>>>
> >>>> Is there something else I should be doing? Your advice will be much
> >>>> appreciated.
> >>>>
> >>>> Regards
> >>>>
> >>>> George
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>
> >>
> >> _______________________________________________
> >> 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
>
>
> _______________________________________________
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> 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 Thu Aug 11 2011 - 07:00:02 PDT
