Dear Jason,
Thank you so much. That clears a lot of things.
Now I am actually running the simulation in my own protein system and it
will be a part of publication that I am currently writing. Since I am kind
of new to this, I thought I would ask you few more questions just to
clarify things in my head.
So if I am planning to run a heating phase of 1 ns and the production phase
(equilibrium phase) for a total of 60 ns. My system is just like ras-raf
but without any ions or GTP. One protein is 59 residues long and the other
is 185 residues long (total 238 residues). I have experimental results that
suggests that the binding is very tight for these two proteins (Kd = less
than 1nM). So, I guess my question is besides what we learn from the given
Amber tutorial, what other areas we can improve on while running
simulation? I know we definitely need longer simulation time. How long is
practical? *Is 1ns of heating and 60 ns of production phase enough for my
system? Or Do I need longer?*
1) Based on my previous question (previous email), what I did for the
tutorial was: I looked at the rmsd and figured after approximately 200
frames the system is fully equilibrated. So I started frame at 200 and
ended at 700 (end) with interval = 5 in my mmpbsa.in script. Is this how
you select the frames every time? Is it only based on RMSD or are there any
other factors that I need to consider while selecting frames for my
calculations?
2) I know higher the interval statistically better for calculations, is 5
? how do we know if it is enough or not? Is there a way we can check after
the PB/GB calcualtion whether the interval was enough? I am guessing we
check the errors.
3) This is the script I am planning to use for my system. There are other
variables that we can us in the script. for eg, indi, exdi, surface tension
and many more. Do we have to change these variables or leave it as DEFAULT?
I know it varies with your system and what you want to accomplish but for
simple PB/GB calculations do we need to consider changing any of these
variables or DEFAULT is just fine?
&general
startframe=200, endframe=700, interval=5,
verbose=2, keep_files=2, strip_mask=':WAT,CL',
/
&gb
igb=5, saltcon=0.150,
/
&pb
inp=1, radiopt=0, istrng=0.15, fillratio=4.0
/
4) During the calculation of PB/GBSA, the command is setup in a way so that
it considers all .mdcrd files for the calculations (*.mdcrd). But my
heating phase does not even get up to 700 frames because it is shorter
(only 1ns). Only my prod.mdcrd has that many frames. So if I stated start
and ending frame as above, how does the system considers the situation that
my heating phase doesn't even have that many frames??
5) Finally, after PB/GBSA calculation is done, what are the variables or
output data that I should be carefully looking at to check any errors or
any possible problems during the calculations?
Sorry for all these questions again. As a beginner, I am just trying to
connect a lot of things here and I apologize in advance if some of these
questions sound stupid.
Thanks you for all your time again.
On Tue, Mar 8, 2016 at 9:39 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Mar 8, 2016 at 2:06 PM, Arati Paudyal <apsilwal123.gmail.com>
> wrote:
>
> > Dear all,
> >
> > I just finished the tutorial for MMPB/GB SA with ras-raf protein and I
> > followed the tutorial. But this time I ran the the equilibrium step for
> > 30,000,000 steps for a total simulation time of 60 ns instead of 500 ps
> as
> > in tutorial. In the tutorial, there are separate production steps run
> for a
> > total of 2 ns. I guess, my questions is, if you run your equilibiation
> > phase for 60 ps already, do I need to run the production step again? I
> > checked everything including rmsd, energy and density and my system is
> > fully equilibriated.
> >
>
> There is really no difference between "equilibration" and "production" in
> terms of simulation protocol. "Equilibration" is simply what we call the
> portion of the production simulation in the beginning that we discard
> because there is a high(er) likelihood that it is not sampling from an
> equilibrium distribution.
>
> So if you ran 60 ns of MD, and you think that (for whatever justification),
> the last 58 ns sample from the free energy surface (i.e., the equilibrium
> distribution), then you should start your MMPBSA.py analyses from the start
> of the 3rd nanosecond.
>
> If NOT, then when we run the mmpbsa.py script, how do we start from the
> > point where the system is already equilibriated? Is it something do do
> with
> > the start and end frames in the script? For eg. following is the rmsd
> plot
> > of my system afte 60ns of equilibriation. I can see the system is
> > equilibriated after about 200 frames. So can I assign my start frame as
> 200
> > and end frame as 700?
> >
>
> I would suggest setting your start frame to 200 or so, as you said, and
> then putting your endframe to the very end of the simulation. You can pick
> a long interval to reduce the number of structures you feed to MMPBSA.py.
> The more time between adjacent snapshots, the less correlated the results
> will be (and therefore, the more statistically significant they will be).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Mar 09 2016 - 06:00:05 PST
