shahid nayeem wrote:
Thanks for quick reply. I have created mutant of a complex by changing
interface residue in VMD. These mutant are experimentally known to show
less binding affinity. I want to reproduce these results with umbrella
sampling. Now I am sending profile and histo file for wt and mutant.
Please suggest where i am wrong.
The PMF curves look poorly converged. Your reaction coordinates are not the
same for both the WT and mutant (you appear to have a far shorter reaction
coordinate for the mutant). The energy minimum is also ill-defined for the
mutant.
As for the reason behind these phenomena, I cannot say, nor do I have time to
sort through your data and try to work it out for you. Refer to the literature,
find similar protocols, and proceed from there.
-Justin
Shahid Nayeem
On Mon, Feb 13, 2012 at 7:15 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
shahid nayeem wrote:
Dear Justin
I am doing umbrella pulling simulation of a protein complex wt
and mutant. I expect mutant to give lower deltG value. I am
attaching a tif file of energy vs time curve of wt and mutant
protein on pulling simulation. These energies are obtained by
g_energy and selecting 11 option which is COM pulling energy. In
this curve the first peak decreases and again rises at longer
time. How many windows should be selected. As expected the peak
of COM pulling energy is lower in mutants. Please explain why
the energy again rises at higher time. Should I use the windows
upto 160ps only because thereafter in both curve there is rise
in energy value. the pull code used is as follows.
What you have obtained is a path-dependent energy that may or may
not signify anything useful - it almost certainly does not. I
cannot offer an explanation of the sharp increase towards the end of
the simulation other than to speculate that your box is of
insufficient size and you're encountering PBC issues.
As for how many windows are necessary, it's also impossible to tell.
You need enough windows to adequately sample the reaction
coordinate. Thus, it is decided based on how far you need to
separate the two species, how strong the force constant is during
the US simulations, the nature of the interactions in the system and
how fast they converge, etc.
-Justin
pull_geometry = distance pull_dim = Y N Y
pull_vec1 = 0.75 0 1
pull_start = yes pull_ngroups = 1
pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1
= 0.01 pull_k1 = 1000
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/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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