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
--
========================================
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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