[gmx-users] problem with downloaded lipid bilayer

Carl-Johan Högberg cjh at physc.su.se
Wed Mar 3 19:41:01 CET 2004

Dear all.

I have some problem with a dmpc-lipid bilayer downloaded from dr 
Tielemans groups site. The file contains 128dmpc lipids and 3655water 
molecules. I have managed to manually create a *.top file and together 
with the downloded dppc128.pdb file created a *.tpr file from grompp. 
When i start the simulation with mdrun i get the following error message:

Warning: Only triclinic boxes with the first vector parallel to the 
x-axis and the second vecto              r in the xy-plane are supported.
          Box (3x3):
             Box[    0]={         nan,          nan,          nan}
             Box[    1]={         nan,          nan,          nan}
             Box[    2]={         nan,          nan,          nan}
          Can not fix pbc.

And when looking at the pdb file it looks like something i should not 
mention here.

I would appreciate any help a can get with this problem.


Carl-Johan Högberg
Department of Physical Chemistry
Arrhenius Laboratory
Stockholm University
S-106 91 Stockholm
Phone: +46-8-162373

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