[EMAIL PROTECTED] 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
for example).
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.
Cheers,
Bruce
--
"Hamewith - the road that's never dreary"
Dr. Bruce F. Milne
CEQOFFUP
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164
4050-047
Porto
Portugal
email: [EMAIL PROTECTED]
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