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 how many lipids did
other people use.
On 07/29/2013 10:31 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).
since you (Justin) you have mentioned that the protein must be completely
inside the membrane to avoid any instability, what must I do to avoid this
problem?
is something wrong with my protein?
The region protruding out is a loop. is it still a problem?
the protein's box size is 4.49101 4.74797 7.29103 (from protein.gro).
Kindly help.
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