Hi,
I have to say that I am definitely not an expert in this subject.
When I have this issue I just use Molmol to add the protons, which I
would assume is based on ideal geometry. For any simulation I would
guess that the proton will move around in and out of the peptide
plane. So, if you can assume that this motion is accurately simulated
which, if done correctly, these fast motions should be then maybe the
average position would be the best for model-free analysis.
Be careful though because this is a whole can of worms you could be
opening here! Model-free analysis (as well as many other theories in
the field) assumes in its theory that you have a defined bond vector
orientation but the analysis implies motion which in turn means the
vector moves again in turn changing the results of the analysis. Note
the circular loop of dependence and the lack of theory addressing this
- this really is not an issue for the faint hearted!
Regards,
Edward
On 10/24/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
Hi Ed
Thanks for the information about the relative PDB orientation and Euler
angles...
For adding hydrogens to a PDB, I wonder what approach is best so that it
can be used (in relax) for non isotropic relaxation analysis. In other
words, what approach would be best to get good NH vector orientations ?
I have a PDB at 1.95 A resolution and without any hydrogen. I tried two
different approaches to get the hydrogens in a good orientation...
1.
Hydrogens were added inside CHARMM and then a short Langevin minimization
(200 ps) was done.
2.
Hydrogens were added inside CHARMM (as for approach 1) and then a molecular
dynamics simulation was performed (by another PhD student) with TIP3P water
and 3 snapshots were taken at time 10, 12 and 14 ns (after 2 ns
equilibration)... I could take snapshots up to 40 ns, but they should be
equivalent to others...
My questions :
What approach do you think is the best to get good NH orientations ?
Would it be relevant to take different snapshots from MD and use them in
separate relax runs ?
Would you suggest another approach ?
Cheers
Sébastien :)
Edward d'Auvergne wrote:
Hi,
The only differences in the analysis should be due to different bond
orientations. The PDB reference frame doesn't matter - this will only
change the values Euler angles of the diffusion tensor and nothing
else. So if the same structure exists in two different PDB frames,
then the difference in the optimised Euler angles will be solely due
to the rotation between the two structures. If you were to change the
PDB frame in any of your files, the final chi-squared value should be
identical to a non-rotated PDB. The differences you do see are
because the relative XH bond orientations in the different structures
are different.
Regards,
Edward
On 8/30/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
Hi,
I am doing different tests with the full_analysis.py script, data at
three magnetic fields and different PDB structures (taken from MD
simulations).
I realized that those different structures give rise to different
optimization times and also to different chi-squared values for the
different diffusion tensors (I have only tried the prolate diffusion
tensor).
I wonder if the structures need to be processed before giving as inputs
for relax. Especially, do the structures need to be centered relative to
their inertia tensor (like with the pdbinertia program that one should
use prior to model-free analysis using ModelFree).
Thanks !
Sébastien :)
--
______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
|| ||
|_______________________________________________|
______________________________________
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______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
|| ||
|_______________________________________________|
______________________________________
Re: PDB orientation