[gmx-users] Re: Problems prior to running lipid-protein simulation

[Mark Abraham]

Bruce Milne wrote:
> You don't have to run pdb2gmx for the whole system at any point 

Probably true.

> (it's 
> not going to work anyway unless you add the POPC parameters to all the 
> force field files and then add the POPC residue to the  .rtp file so 
> that  pdb2gmx can recognize it).

Not quite true. The contents of the .itp files don't matter to pdb2gmx 
since it writes a .top file that #includes them. So you need to have a 
working POPC entry in an .rtp file for pdb2gmx, and later on, when using 
grompp, you'll need the former contents of the .rtp file to correspond 
to stuff the .itp files. The latter you need even without using pdb2gmx, 
of course.

Mark