[gmx-users] About Choice PDB

[Justin A. Lemkul]

vidhya sankar wrote:
> Dear justin,,
>                     Thank you for your immediate reply.
> Which PDB is suitable Either X-ray PDB  (brookavean protein data bank) 
> or NMR PDB  to study the effect of ionic strength on protein.
> If i use x-ray PDB
> will it affect the result though i solvate and neutralise the PDB before 
> energy minimization, Equilibration and MD ?

Any structural model is going to have inherent limitations as far as resolution, 
environment in which it was determined, etc.  I doubt that a convincing argument 
can be made either way as to whether one technique is inherently better for a 
study that may or may not depend on it (I have no idea on "the effect of ionic 
strength on protein" means - it's quite vague).

Please make sure to keep your questions focused on Gromacs issues.

-Justin


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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