[gmx-users] problem with downloaded lipid bilayer

Carl-Johan Högberg cjh at physc.su.se
Thu Mar 4 10:28:01 CET 2004

Hi again

No the only output i get is the following:

Back Off! I just backed up step0.pdb to ./#step0.pdb.1#
Wrote pdb files with previous and current coordinates
Warning: Only triclinic boxes with the first vector parallel to the 
x-axis and the second vector 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.

This message is repeted over and over.

My *.top file looks like this:

; Include forcefield parameters
#include "ffgmx.itp"

; Include chain topologies
#include "dmpc.itp"

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

[ system ]
; Name
Pure DMPC bilayer with 128 lipids and 3655 water molecules

[ molecules ]
; Compound        #mols
DMPC              128
SOL               36


Best regards

David van der Spoel wrote:

>On Wed, 3 Mar 2004, Carl-Johan Högberg wrote:
>>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:
>most likely a topology issue. have you checked the energies before the 

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

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