Thank you so much sir.
the entire thread was highly useful.
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On 7/29/13 9:03 PM, pavithrakb wrote:
I would have made a blunder by selecting the POPE membrane.
But, that paper (one which used POPE for human protein) was published in
ACS-Journal of Chemical Information and Modeling.
I thought following high standard papers are trust worthy.
Thank you so mu
I would have made a blunder by selecting the POPE membrane.
But, that paper (one which used POPE for human protein) was published in
ACS-Journal of Chemical Information and Modeling.
I thought following high standard papers are trust worthy.
Thank you so much sir. I will start learning the basics
On 7/29/13 9:10 AM, pavithrakb wrote:
sir,
the reason for selecting POPE doesn't have much valid reason. I mean, I have
referred previous works and in the recent work they have used POPE membrane
for my protein (the exact protein) simulation. I have searched literature on
selecting a membrane f
sir,
the reason for selecting POPE doesn't have much valid reason. I mean, I have
referred previous works and in the recent work they have used POPE membrane
for my protein (the exact protein) simulation. I have searched literature on
selecting a membrane for simulation to know/understand why they
On 7/29/13 4:31 AM, pavithrakb wrote:
Thank you both of you (Justin and Albert) sir.
Initially I was using dppc128 and now I changed to POPE 340 and still my
protein (its a GPCR protein) protrude out of the membrane (the same region;
two amino acids).
Out of curiosity, why have you chosen POP
superimpose your receptor PDB files with related structure OPM database
center your lipids in 0 by editconf command in gromacs
then you GPCR would be in the center of the lipids.
PS: 340 lipids is too big for a single GPCR, 140~160 would be enough
before g_membed. You'd better read paper to see
Thank you both of you (Justin and Albert) sir.
Initially I was using dppc128 and now I changed to POPE 340 and still my
protein (its a GPCR protein) protrude out of the membrane (the same region;
two amino acids).
since you (Justin) you have mentioned that the protein must be completely
inside the
Just a piece of advices: you can consider equilibrate a lipids system
which is large enough for your protein. This will save you huge amount
of time on using tricks to add water later or enlarge the lipids.
The system MUST BE IN PBC BOX for the g_membed input coordinate,
otherwise your job w
On 7/7/13 10:52 PM, pavithrakb wrote:
Dear Sir,
Thanks so much..
now what's the solution? Should I increase the box size?
Yes. If the protein protrudes "out" of the central image, then you will have an
unstable system due to atomic overlap as well as violations of the minimum image
convent
Dear Sir,
Thanks so much..
now what's the solution? Should I increase the box size?
Already I have centered the protein and fixed the POPE membrane size.
Can you tell me how to increase the box size? or is there any other
solution?
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