On 2/18/13 9:54 AM, Biswajit Gorai wrote:
Dear Justin,
Thanks a lot for your reply.
As u mentioned, I edited the mass as follows:
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB ch
argeB
1 CA 1 GDM C1 1 0.99610 12.010000
2 N2 1 GDM N1 2 -0.94930 14.010000
3 H 1 GDM H1 3 0.47530 1.008000
4 H 1 GDM H2 4 0.47530 1.008000
5 N2 1 GDM N2 5 -0.94930 14.010000
6 H 1 GDM H3 6 0.47530 1.008000
7 H 1 GDM H4 7 0.47530 1.008000
8 N2 1 GDM N3 8 -0.94930 14.010000
9 H 1 GDM H5 9 0.47530 1.008000
10 H 1 GDM H6 10 0.47530 1.008000
I am dealing with a small basic protein of 60 aa.
It is a very stable protein which maintains its structure even at 8 M Urea
but 5M GdmCl can denature it (experimentally).
In-silico (simulation) studies have done in hundreds of ns to denature
their target proteins using chemical denaturants.
Unfortunately, I don't have such computational power.
I already denatured my protein at 423 K around ~40 ns.
So combination of both (chemical and physical denaturants) should able to
produce the expected result
atleast below 40 ns or so (within available resources).
But that is not happening, most surprisingly, even the temperature effect
nullifies.
Showing GdmCl producing counteraction to temperature, which experimentally
doesn't valid for my target.
The only advice I would provide is to follow an established protocol rather than
mess around haphazardly with things you hope will work. The other plain fact is
that if other simulations require hundreds of ns to manifest the desired
behavior, you should likely expect the same. You should stick to a given set of
experimental conditions and try to model it rather than trying to deconvolute
complex contributions to denaturation after the fact.
-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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