[gmx-users] rmsf question

Mark Abraham Mark.Abraham at anu.edu.au
Mon Mar 15 09:00:02 CET 2010

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.


> (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.Abraham at 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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