On 16/03/2010 8:17 PM, XAvier Periole wrote:
On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote:
Dear Mark and Tjerk,
Thank you for your comments.
If I correctly uderstand the RMSF computed on C-alpha in PDB NMR
structure, is a measure of the uncertanty in resolving the structure.
Well, the "uncertainty of the NMR experiment" would be strongly correlated
with the dynamics of the system in solution, which in a sense reflects
its fluctuations.
... *if* there's reason to believe that the NMR ensemble reflects the
Boltzmann ensemble. I've no idea how such software works, but I could
certainly imagine algorithms that produced a set of plausible structures
by varying things that have little or nothing to do with physics...
starting points for constrained geometry optimizations, for example.
Mark
This is different from an actual "uncertainty" of the experiment.
Compared to this the RMSF of C-alpha computed from a MD trajectory
reflects the geometric fluctuations of the backbone in the Boltzmann
distribution of states in the generated ensemble.
The uncertanty in the NMR structure can be influenced by the thermal
fluctuations in the backbone geometry.
Only in this respect the comparison of the two makes sense.
Is this correct?
Many thanks again for your comments!
Andrei
On Mon, Mar 15, 2010 at 10:00 AM, Mark Abraham
<mark.abra...@anu.edu.au> wrote:
On 15/03/2010 6:45 PM, Andrei Neamtu wrote:
Dear Mark,
Thank you very much for your response.
What I meant was to obtain a RMSF plot form PDB mediated on each
residue and to compare with a RMSF plot mediated on each residue
obtained from a MD trajectory.
I do not compare a frame from PDB with a frame from MD trajectory.
Sure. I didn't imply you needed or wanted to.
g_rmsf -f your.pdb -s some_suitable.file -n some.ndx
g_rmsf -f your.xtc -s some_other_suitable.file -n some_other.ndx
In certain cases you'll get to use the same -s or -n, or have to
juggle atom
orders.
So, in the PDB file each 'frame' (MODEL) in the NMR file has the same
order and number of atoms.
This is also true for the MD trajectory.
In the end i compare the two plots to see if the residues along the
chain have comparable 'flexibility'
Is necessary in this case to have a correspondence between the order
of atoms in PDb and in MD trajectory?
In this sense the comparison makes sense? (I mean if I do the residue
mediation)
You just need to make sure you are comparing equivalent things. If
you just
want (say) a C-alpha RMSF plot, then you can go ahead and do that if the
index groups work. If you want all-atom RMSF then you might have some
more
fiddly work to do.
Mark
(The PDB is a NMR structure and so it has the hydorgen added and no
missing side chains. And, it has the same number of atoms as the gro
file generated with pdb2gmx. And also the same number of atoms in the
corresponding residues.)
Many thanks,
Andrei
On Sun, Mar 14, 2010 at 3:16 PM, Mark Abraham<mark.abra...@anu.edu.au>
wrote:
On 14/03/2010 7:47 PM, Andrei Neamtu wrote:
Hi,
is there a rapid way to compute RMSF on an NMR ensemble from a PDB
file?
Yes, but that's not your problem, it seems :-)
g_rmsf needs a .tpr file.
Not true. Inspect the lines in g_rmsf -h describing the file types
suitable
for -f and -s. This is a fairly general GROMACS phenomenon.
This is OK with the MD trajectories but if I
want to compare MD ensemble one with the NMR RMSF ensemble
fluctuations from the original PDB this is not possible.
That can be a trickier proposition. You need at least the atom
order to
correspond to make such a comparison.
If the original atom names are suitable for defining the default
groups,
then you might be in business. Otherwise, you'll need to construct
suitable
input for -s (and maybe -n), and see if it matters whether
different atom
names in -f matter.
Mark
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