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
> >>
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> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Aug 10 2011 - 20:30:04 PDT
