[gmx-users] grompp error:Invalid order for directive defaults

[Dongsheng Zhang]

Dear David,

Thank you for your help. It makes sense now. However, it leads me to ask
you another question:

My poly.itp is got from PRODRG server. It has gromos type force field
paramters. Do you think my cnt.itp has to be gromos type force field
format as well (atomtype, bondtype etc)? In fact I used oplsaa to get my
cnt.itp, that's the reason I need two defaults sections.


Best Wishes!


Dongsheng


On Mon, 2006-06-12 at 17:20 +0200, David van der Spoel wrote:
> Dongsheng Zhang wrote:
> > Dear David,
> > 
> > Thank you very much for your reply. I am sorry to tell you that I get
> > the same error mesasge after I try your suggestion. Any other
> > suggestion?
> 
> 
> check the manual, check the archives.
> 
> you can not have two defaults sections.
> 
> > 
> > I think the question is if we can put two sets of force field parameters
> > in two itp files which will be included in one topology file.  From the
> > source code  (topio.c line 381 - 390):
> > 
> > 	  if (DS_Check_Order (DS,newd)) {
> > 	    DS_Push (&DS,newd);
> > 	    d = newd;
> > 	  }
> > 	  else {
> > 	    /* we should print here which directives should have
> > 	       been present, and which actually are */
> > 	    gmx_fatal(FARGS,"Invalid order for directive %s, file \"%s\", line
> > %d",dirstr,curfile,curline);
> > 	    /* d = d_invalid; */
> > 	  }
> > 
> > It seems gromacs does check if a same directive has been present. Is it
> > correct?
> > 
> > 
> > Best Wishes!
> > 
> > 
> > Dongsheng
> > 
> > 
> > On Mon, 2006-06-12 at 09:35 +0200, David van der Spoel wrote:
> >> Dongsheng Zhang wrote:
> >>> Dear GMX users,
> >>>
> >>> I'd like to study the interaction between carbon nanotube and a polymer
> >>> chain. I have made cnt.itp for the nanotube and poly.itp. Both itp files
> >>> contains force field parameters (such as [ defaults ], [ atomtypes],
> >>> [ bondtypes ]), in this way, I don't need to include any force field in
> >>> my topology file (but it will include *.itp) and it is much easier to
> >>> modify the parameters. For use nanotube or polymer alone as my system, I
> >>> can use grompp to process .gro, .itp, .top to get .tpr file. If I use
> >>> nanotube and polymer together as my system, grompp give me the following
> >>> error message:
> >>>
> >>> Invalid order for directive defaults, file ""poly.itp"", line 16 
> >> divide your itp files into two, force field and molecule description
> >>
> >> then in your .top file you include all four. chapter 5 in the manual
> >>
> >>> line 16 is [ defaults ], so I am thinking maybe I can't have
> >>> [ defaults ] in each of two itp files. If I delete [ defaults ] in the
> >>> second itp file. It will complain [ atomtypes] in the second itp file.
> >>> It seems I can't put force field parameters in two itp files which will
> >>> be included in one topology file. Could anyone tell me if my guessing is
> >>> correct? If so, why does gromacs prevent it? 
> >>>
> >>> Thank you in advance! If you need more information, I will be more than
> >>> happy to provide it.
> >>>
> >>>
> >>> Best wishes!
> >>>
> >>>
> >>> Dongsheng
> >>> _______________________________________________
> >>> gmx-users mailing list    gmx-users at gromacs.org
> >>> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>> Please don't post (un)subscribe requests to the list. Use the 
> >>> www interface or send it to gmx-users-request at gromacs.org.
> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
>