Hello,
Oliver is right, you can supply different trajectories for all of the
different parts (complex, receptor, and ligand), but you can't do "stability
calculations" where you only specify the complex, like you can in mm_pbsa.pl
.
Hope this helps,
Jason
On Fri, Jul 23, 2010 at 6:55 AM, Oliver Grant <olivercgrant.gmail.com>wrote:
> In MMPBSA.py the 'single trajectory approach' means you input one
> trajectory of your complex. The 'different trajectory approach' or
> ''multiple trajectory approach' means you can supply separate trajectories
> of your ligand alone in solution and your receptor alone in solution to
> hopefully give a more accurate ensemble of conformations when calculating
> the ligand desolvation and receptor desolvation parts.
>
> I'm not sure what you are trying to find out by running the ligand alone.
> Is
> it desolvation energy?
> *"it seems there is no way that mmpbsa.py can calculate for me the binding
> energy for a ligand alone, or even a receptor alone.*"
> Could you explain what you are trying to achieve from this? To calculate
> binding energy, the ligand/receptor will have to bind to something.
>
> All the best,
> Oliver
>
> On 23 July 2010 05:16, Amor San Juan <amorsanjuan.yahoo.com> wrote:
>
> > Calculation of binding energy has two approaches: 'single trajectory
> > approach' and 'different trajectory approach'. The mmpbsa.pl module can
> do
> > both. I want to know from the developer of mmpbsa.py if it can also do
> both.
> >
> > This is the case of what I want to calculate. My input file does not
> > contain complex, just a standalone ligand, or standalone receptor. Can
> > mmpbsa.py perform calculations if my input file only include a ligand ?
> >
> > In accord with the manual, there are 6 mandatory command lines for
> > mmpbsa.py which include:
> >
> > -i input file \
> > -o output file \
> > -cp complex_prmtop \
> > -rp receptor_prmtop \
> > -lp ligand_prmtop \
> > -y mdcrd file \
> >
> > In my case, the only input I have is a ligand, no complex and no
> receptor.
> > Since abovelisted are mandatory fields, it seems there is no way that
> > mmpbsa.py can calculate for me the binding energy for a ligand alone, or
> > even a receptor alone. I tried several tests but it wasnt successful at
> all.
> > So before I give up, I want to confirm from developers if this case can
> not
> > be handled by mmpbsa.py.
> >
> > Amor
> >
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jul 23 2010 - 05:30:03 PDT
