[gmx-users] rmsf question

[Andrei Neamtu]

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.
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.Abraham at 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.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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