[gmx-users] rmsf question

[Mark Abraham]

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.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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>