I also suggest doing a cluster analysis before doing this kind of melting
curve. If the "native" is only 10% at low T, it's entirely possible that
your simulation setup (force field, solvent, etc) actually prefer a
different structure. What I mean is - is the 90% that is not native just a
mix of unfolded things, or is it possible that there is a big cluster of a
specific incorrect conformation and the "native" one is a minor conformer?
It's important to know if your experimental structure just isn't stable
enough in the simulation, or if the simulation is predicting the wrong
structure entirely.
On Tue, Sep 24, 2013 at 10:56 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Tue, Sep 24, 2013 at 6:44 AM, Gargi Borgohai <gargib2011.gmail.com>
> wrote:
> > TEMPLIST=`cat temperatures.dat`
> >
> > for T in $TEMPLIST ; do
> >
> > trajin remd.mdcrd.001 remdtraj remdtrajtemp 267.0
> > trajout remd.Ttraj.267
>
> This script as written will give only the trajectory at 267 K. It
> should be something like:
>
> trajin remd.mdcrd.001 remdtraj remdtrajtemp $T
> trajout remd.Ttraj.$T
>
> FYI you may be interested in trying the 'ensemble' command in cpptraj,
> which will sort and process all temperatures at once. For example, the
> input to cpptraj in your case would be (no 'for' loop required):
>
> ensemble remd.mdcrd.001
> trajout remd.Ttraj
>
> You would obtain trajectory files 'remd.Ttraj.X', where X corresponds
> to a position sorted temperature list starting from 0. You can also do
> some simple actions on the entire ensemble at once (calculate
> distances, rmsds etc).
>
> > While calculating average value of helical fraction
> > (averaged over all frames) for each temperature the value is found to be
> > near about same for each temperature. And when population of "native
> state"
> > was calculated for each temperature, it was found to decrease with
> > increasing temperature (which is expected). But this % of population at
> the
> > lowest temperature (i.e. at 267K) is very small, its about ~10% of the
> > total frames of the whole temperature based trajectory (which is obtained
> > from remd.Ttraj.267). But this is not expected. I may have done some
> > mistake either in finding out temperature based trajectory or in finding
> > the population of "native state" at each temperature. Will you please
> help
> > me in choosing the right pathway to calculate the same? This will be a
> > great help for me.
>
> Unfortunately there is no easy answer here, and without knowing more
> about what your system actually is I can only speculate. Do you have
> experimental evidence for what the population should be at 267 K? Also
> 267 K is getting pretty cold, and some proteins do undergo a
> phenomenon known as "cold denaturation" (although usually a
> temperatures a little colder). If you started your REMD simulation
> with a conformation other than native it could be that you haven't run
> long enough and your ensemble simply hasn't converged. Do you have at
> least one other independent REMD simulation that gives similar
> results?
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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Received on Tue Sep 24 2013 - 08:30:02 PDT
