[gmx-users] Re: problem in g_membed

[Albert]

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.