The solvated prmtop is used by ptraj to remove water molecules and ions. The
best guess masks for the receptor and ligand are determined by trying to
locate the ligand residue sequence (found in ligand.prmtop) within the
complex.prmtop residue framework. Thus, it sounds like this should work for
your system correctly as long as the ligand and receptor are in the same
orders with respect to one another in the solvated_complex.prmtop and
complex.prmtop files.
Good luck!
-Bill Miller
On Mon, Mar 15, 2010 at 5:00 AM, s. Bill <s_bill36.yahoo.co.uk> wrote:
> Dear AMBERThanks so much for your help.In fact, I found I made a mistake in
> my prmtop files.I was wondering, the following masks in the output dat file
> of MMPBSA.py calculation have been taken based on which prmtop file
> (Complex,Solvated Complex, or simulation.mdcrd file) in case, these files
> are not have the same residues in the same order.
> |Best guess for receptor mask: ":1-176"|Best guess for ligand mask:
> ":177"|Ligand residue name is "X1"
> In other words, is it a problem if my solvated_complex.prmtop doesn't have
> the same sequential residues as in complex.prmtop, where there are some
> water molecules between the end of the receptor and the ligand, but I
> removed these water molecules and rebuilt my complex.prmtop but all my mdcrd
> data has been generated based on solvate_complex.prmtop with water between
> receptor and ligand.I think MMPBSA.py uses ptraj to extract snapshots from
> mdcrd and then strip out the water molecules, so in this case there will no
> be a difference between my prmtop files, am I right?Thanks again for your
> help.Sincerely;S. Bill
> --- On Sun, 14/3/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] MMPBSA.py problem
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Sunday, 14 March, 2010, 16:47
>
> On Sun, Mar 14, 2010 at 5:56 AM, s. Bill <s_bill36.yahoo.co.uk> wrote:
> > Dear AMBERI am trying to use MMPBSA.py to calculate the binding energy,
> where mm_pbsa.pl is not available for my system because of existence of
> zinc ion in my system. (I do know I can implement it in
> mm_pbsa_calceneent.pm file).But, the problem for mmpbsa.py is that, I have
> submitted my mmpbsa.in file as following
> > Input file:Input file for running PB and GB in parallel&general
> endframe=20, verbose=1, /&gb igb=2, saltcon=0.000/&pb istrng=0.000, /
> > It gives me an output without a
> calculations:|Input file for running PB and GB in parallel|&general|
> endframe=1, verbose=1,|/|&gb| igb=2, saltcon=0.000|/|&pb|
> istrng=0.000,|/|--------------------------------------------------------------|Solvated
> complex topology file: SolvatedComplex.prmtop|Complex topology file:
> Complex.prmtop|Receptor topology file: Receptor.prmtop|Ligand
> topology file: Ligand.prmtop|Initial mdcrd(s):
> Data.mdcrd||Best guess for receptor mask: ":1-292"|Best guess for ligand
> mask: ":293"|Ligand residue name is "X1"||Calculations performed using 1
> frames.|Poisson Boltzmann calculations performed using internal PBSA solver
> in sander.||All units are reported in
>
> kcal/mole.--------------------------------------------------------------------------------------------------------------------------------------------------------------
> >
> > I have followed the mmpbsa.py thread discussing this problem on AMBER
> list, so I tried using initial_traj=1 without specifying -sp prmtop
> file. But, it gives me the following error:Error: Sander output is missing
> values! BOND = ************* ANGLE = 255832.2695 DIHED =
> 9628.0187
> > How can I solve this issue?Also, I was wondering should I include the
> crystallic water molecules and ions in my receptor prmtop file.Thanks in
> advanceS. Bill
>
> Try visualizing your system. Look at the mdcrd files created by
> MMPBSA.py in some type of visualization program with the corresponding
> prmtop files (VMD works well). This result is probably due to the
> fact that the
> prmtop files and coordinate files are not matching up
> (so if you try to visualize them, you will get a mess).
>
> Good luck!
> Jason
>
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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>
>
>
>
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Received on Mon Mar 15 2010 - 06:00:16 PDT
