On 5/15/13 7:14 PM, Payman Pirzadeh wrote:
Hello,
I am simulating a protein using side chain pKa values estimated from
PROPKA based on crystal structure of the protein. I re-estimated the pKa
of side chains after running 10 independent replica of 50ns (500ns in
total) of NPT simulations. It turned out that the average pKa of a
surface Glu was overestimated in the crystal structure (protonated), and
needs to be reconsidered (not protonated). I was wondering how I can
re-assign the protonation state of this single residue without going
through pdb2gmx (or may be I have to) to keep the current conformation
of the protein and currently equilibrated solvent molecules? Is there a
way to continue the current simulations I have and only change the
charge of this single surface Glu?
No, because doing so (1) isn't possible and (2) doesn't make sense. You're not
just changing charges, you're deleting an atom. You have to generate a new
topology with pdb2gmx, simple as that. You can easily just run the whole system
through pdb2gmx to preserve the configuration (provided you don't have any other
weird molecules involved that pdb2gmx won't like, but you can also work around
that easily). Preserving the coordinates is relatively insignificant compared
to the fact that there is no way to preserve the previous ensemble. You can't
change the topology and then try to continue from a previous state (i.e.,
checkpoint file), so you have to re-equilibrate anyway.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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