Thanks to Mark and Chris ! :) Zaz.
--- Mark Abraham <[EMAIL PROTECTED]> 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 > > _______________________________________________ > 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 > ____________________________________________________________________________________ Novo Yahoo! Cadê? - Experimente uma nova busca. http://yahoo.com.br/oqueeuganhocomisso _______________________________________________ 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
