: Re: [gmx-users] Membrane protein insertion
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Hi,
I used this method recently and I was experiencing the same errors. As
Mark suggested, makes sure your protein survives an energy minimisation.
My error
Hi,
I used this method recently and I was experiencing the same errors. As
Mark suggested, makes sure your protein survives an energy minimisation.
My error was a result of poor preparation of the .pdb file before running
pdb2gmx. My .itp file contained a long bond between the C and N termini of
Hi all,
I want to insert a membrane protein into a model bilayer and I've tried
several methods. The more straightforward seems to be Memembed, which
gives an orientation to the membrane. On the other hand this method only
outputs the membrane as dummy balls. How to translate this orientation
Hi,
Something isn't stable. Check that your membrane protein survives a vacuum
EM (at least). And check your parameter settings for inflategro.
Mark
On Mon, Aug 24, 2015 at 9:53 AM Yasser Almeida Hernández
yasser.almeida.hernan...@chemie.uni-hamburg.de wrote:
Hi all,
I want to insert a
] Membrane protein insertion/orientation
methods
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cago0fv_f342oxfcqtgrwn4s72bxhe+pa0e+kz4-uzgw9mou...@mail.gmail.com
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Hi there,
Lambada + InflateGRO2 is a good combination.
As for which method is the best one is difficult to say
Hi all,
Among the methods available, which one is the best/more rigorous/popular
for membrane protein insertion/orientation in model bilayers
(InflateGRO, Memembed, g_membed, etc.)?
Thanks in advance
Yasser
--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular
Hi there,
Lambada + InflateGRO2 is a good combination.
As for which method is the best one is difficult to say. If you read the
articles you will have a nice idea of the pros and cons of each method and
then you can decide by yourself. The only thing I can say is that after
reading them all I
Hi Yasser,
InflateGRO and g_membed do not predict the insertion or orientation, but
require the protein to be oriented already. With InflateGRO2, Christian
Kandt also brought out LAMBADA which may help aligning a protein with the
membrane. memembed is also an orientation predictor. However, I
