[gmx-users] Lipid-protein force field problem.

[zazeri]

Thanks to Mark and Chris ! :)
 Zaz.


--- Mark Abraham <mark.abraham at anu.edu.au> escreveu:

> > Hi to all ! :D
> >
> > I've been trying to work with membrane
> > DPPC+peptide+waters simulation.
> > Following the "example.top" from Tieleman's
> website,
> > I've done my topology as:
> >
> > #include "ffgmx.itp"
> > #include "lipid.itp"
> > #include "dppc.itp"
> > #include "protein.itp" ;(inside it has been
> written
> > #include "ffG43a2.itp")
> > #include "ions.itp"
> >
> > And I've found:
> > "Fatal error:
> > Found a second defaults directive, file
> "lipid.itp",
> > line 9".
> 
> Read chapter five of the manual to find out what a
> defaults directive is
> and why you can't have two of them. Then don't
> #include more than one file
> that has a default directive. Further, don't mix
> force fields (such as
> ffgmx and ffG43a2 above). See
> http://wiki.gromacs.org/index.php/Force_Fields for
> more info.
> 
> > When I comment the line 9 and execute grompp
> again:
> 
> That might help you diagnose the problem, but it's
> vanishingly unlikely to
> fix it...
> 
> > WARNING 1 [file "lipid.itp", line 13]:
> >   Overriding atomtype LO
> > .
> > .
> > .
> > WARNING 12 [file "lipid.itp", line 24]:
> >   Overriding atomtype LC2
> >
> > So I've decide to comment #include "lipid.itp" in
> the
> > topology file:
> >
> > "Fatal error:
> > Invalid order for directive defaults, file
> > ""ffG43a2.itp"", line 4".
> 
> Hmmm, what do you know? The same error... See above.
> 
> > I've tried several things such as to change the
> order
> > of includes, etc and nothing has solved the
> > problem(s)!
> >
> > Therefore I've decided to make a force field with
> > ffgmx's parameters (to describe the lipids
> > interactions) +
> > ffg43a2's parameters (to describe the peptide
> > interactions).
> 
> Do you have a basis for knowing that these will
> cooperate appropriately?
> 
> > I've done the field following the
> > rules:
> >
> > Interactions between:
> > lipid - lipid: gmx
> > lipid - water: gmx
> > lipid - protein: gmx
> > protein - water: 43a2
> > protein - protein: 43a2
> > lipid - ions: gmx
> > protein - ions: 43a2
> > ions - ions: gmx
> > ions - water: gmx
> > water - water: gmx
> >
> > In the topology file I've written:
> > #include "ffG43a2mod.itp" ;(modified)
> > #include "dppc.itp"
> > #include "peptide.itp"
> > #include "spc.itp"
> > #include "ions.itp"
> >
> > And I've had to face this error:
> > Generated 846 of the 2080 non-bonded parameter
> > combinations
> > WARNING 1 [file "dppc.itp", line 223]:
> >   No default Ryckaert-Bell. types, using zeroes
> > .
> > .
> > .
> > WARNING 12 [file "dppc.itp", line 234]:
> >   No default Ryckaert-Bell. types, using zeroes
> > WARNING 13 [file "dppc.itp", line 239]:
> >   No default Ryckaert-Bell. types, using zeroes
> > .
> > .
> > .
> > WARNING 24 [file "dppc.itp", line 250]:
> >   No default Ryckaert-Bell. types, using zeroes
> >
> > I think that it happens because I didn't define
> the
> > "bonded parameters" from ffgmxbon.itp to
> > ffg43a2modbon.itp.
> > In afirmative case, how do I do to convert and
> include
> > them? Note it's not enough copy and paste! :P
> >
> > As you can see, I've tried to apply all tips
> described
> > in the gmx-users list e other like to make a
> mixture
> > gmx-43a2 force field using brute force.
> >
> > So please, what am I doing wrong?
> 
> Not understanding how force fields work in general,
> and how this is
> implemented in GROMACS. You should read chapter five
> of the manual for the
> latter, and a good textbook for the former :-)
> 
> Mark
> 
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