> 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
