[gmx-users] To Tsjerk "Starting a simulation of a peptide lipid bilayer"

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Apr 26 09:26:57 CEST 2007

In your .top file there will be an #include "ffsomething.itp" which
contains a [defaults] directive and [atomtypes], etc, etc. Then your
lipid.itp is included which contains the same information. Gromacs
doesn't like that (which you could have known by reading chapter 5
thoroughly, and giving your files a good look, noting that #include
just puts in all the contents of the file to be included in the place
of the statement). That [default] you mention is at line 9 of
lipid.itp, but shouldn't be there. The message couldn't be any
clearer. Before lipid.itp is #included there must already be a
[default] section. If it doesn't say so explicitly in the file
#including "lipid.itp", there will be another #include before which
has a default section. THINK! There's so much to gain by understanding
file formats, which is a must when using a scientific program. There's
also much to gain by understanding force fields, which is a must when
doing molecular simulations.



On 4/26/07, nur avneet <nuravneet at yahoo.co.in> wrote:
> Dear Sir
> I have checked the links you gave and also checked my files ...the ffgmx.itp
> has not been included several times....
> the lipid.itp file has a line
> [default]
> 1    1
> [atomtypes]
> .......
> What does the 1   1   under the default section imply...
> and i still cant remove the problem of "Found a second defaults directive,
> file "lipid.itp", line 9
> regards
> nur
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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