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
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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