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
>
>
>
>
> _______________________________________________
> 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
Received on Fri Jul 23 2010 - 04:00:05 PDT
