[gmx-users] rmsf question

[XAvier Periole]

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.
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.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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