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
>
>
>
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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 Mon Mar 15 2010 - 02:30:07 PDT
