Hi Maite,
After removing water molecules, you forgot to change the number of
atoms listed in the second line of the file. Editconf expected more
atoms to come, but ran into the box (the line you see in the error).
Try to get a bit familiar with the file formats of Gromacs. That can
often help to solve problems.
Best,
Tsjerk
On 3/14/07, maite lopez <[EMAIL PROTECTED]> wrote:
Hi:
I am working on peptide-membrane simulation under lipid (DPPC, from
Peter Tieleman group site). I've solvated the system using the x and y
vectors of the initial box (membrane box), but i increased the vector
in the z axes . I've
eliminated the water molecules that are interacting with the apolar coils of the
lipids, but when i try to reorder the atoms with the editconfig command it gives
this error :
Fatal error:
Invalid line in peptide_dppc64_water.gro for atom 20704:
4.72500 4.23200 12.00000
this is a water atom. I eliminated this water molecule and the same
error comes. The line format is ok.
If i eliminated in the initial .gro only a water molecule that it is
interacting with
lipids the same happen.
i visualizated the system and these atoms aren't in contact.
I've done the last steps because when i run a MD of the unmodified system,
the water molecules that are interacting with the apolar coils of the
lipids form clusters between the monolayers.
How can i eliminate this molecules or solvate the system only in the z axes?
I want to add more water molecules and to equilibrated other membranes
of this site, but i'll always obtain water molecules between the
monolayers.
Any help will be highly appreciated.
Maite
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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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