[gmx-users] Re: Problems prior to running lipid-protein simulation
bfmilne at ff.up.pt
Thu Oct 11 14:35:43 CEST 2007
gmx-users-request at gromacs.org wrote:
> 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.
Good point. I was only considering the case where you want pdb2gmx to
provide you with a complete .top file that needs no additions and takes
all its parameters from the same place (as you would get for a protein
Anyway, if you have the .itp files then I think it is easier to simply
add the required #include lines to the protein.top file so that it
covers all the molecule types in your coordinate file without trying to
get pdb2gmx to recognize the lipids.
"Hamewith - the road that's never dreary"
Dr. Bruce F. Milne
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164
email: bfmilne at ff.up.pt
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