Jason,
I feel so stupid now!!
I didn't think through this. Obviously, like you mentioned, I had mutant
ligand and mutant receptor switched in my script. This is what happens when
you simply copy and edit the script from tutorial without thinking
thoroughly. I wasted almost an entire week asking for help and trying to
figure things out. I was so focused on fixing and looking at number of
atoms in topology file that I completely missed the very basic flag in the
script.
The following was the script from tutorial. The only thing I had to do was
to change "mr" at the end to "ml" , just like what you said. It is running
now and I hope I don't get any more errors here.
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -sp ras-raf_solvated.prmtop -cp
rasraf.prmtop -rp ras.prmtop -lp raf.prmtop -y *.mdcrd -mc
rasraf_mutant.prmtop -mr ras_mutant.prmtop
I greatly appreciate your time and concern on this!!
On Wed, Apr 13, 2016 at 10:01 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Apr 13, 2016 at 6:22 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
>
> > Jason,
> > Thanks for your reply.
> >
> > I checked the number of atoms for my system and it is as follows:
> >
> > Mutant_complex: 3930
> > Mutant_A : 3021
> > B: 909
> >
> > For wild type:
> > Wild_complex: 3944
> > A : 3035
> > B: 909
> >
> >
> > There is difference in atom numbers between prmtop from wild type Vs
> Mutant
> > for complex and protein A but isn't the change in atom number expected
> as
> > we are deleting extra atoms to mutate to alanine? The wildtype nA + nB =
> > number of atoms in the wildtype complex. Same for mutant as well. But the
> > error is saying that it is not the case.
>
>
> > I also tried to manually change the atom number in mutant to match the
> atom
> > number of the wild type but got different error message. Any thoughts on
> > this would be helpful.
> >
>
> Never change the contents of the prmtop file (unless you are absolutely
> certain you know what you're doing... and even then, still don't).
>
>
> > Also, you mentioned about changing the flags in the command line in the
> > previous email. Do you mind explaining that a little bit more? All the
> > receptor and ligand protein are already specified. So I was wondering
> what
> > else we could change/check for flags?
> >
>
> Since the numbers you showed above *are* consistent, I suspect you have a
> typo in your command-line. Look for a place where you may have
> accidentally swapped mutant or wild-type prmtop names. Since you've never
> posted the command-line that you used, I can't help spot anything.
>
> The error message you are hitting is a *very* simplistic check. It takes
> the atom numbers from each prmtop (the same numbers I had you look for in
> the prmtop file), adds them up for the receptor and ligand, and checks that
> it is the same number as in the complex. If it's not, it prints the error
> you're seeing. There is very little room for a bug in this particular
> check (especially since it's known to work correctly in the tests and
> tutorial). I strongly suspect you are making a mistake somewhere in your
> command-line that will appear obvious once you see it.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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>
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Received on Thu Apr 14 2016 - 05:00:04 PDT
