[gmx-users] protein membrane simulation

[Chris Neale]

As mentioned by another user, you need POPC in the [ molecules ] 
section. In addition, I see a lack of reference to popc.itp in yout .top 
file. If it is truely absent, this next bit is important.

You have referenced this link:
1) http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html
and that page includes a link to:
2) http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html
and that link includes the following information:

######################

4. make a topology file like this:

#include "ffoplsaa.itp"
#include "myprotein.itp"
#include "spc.itp"
#include "pope.itp"

[ system ]
system_name

[ molecules ]
; Compound        #mols
Protein             1
POPE              299
SOL              8991

######################

But your email doesn't mention popc.itp. Download that file and include it.

If you did miss that bit then I would recommend going back through the 
instructions to see if you missed something else as well.

Also, I would at least think about doing something like this:
http://www.gromacs.org/pipermail/gmx-users/2006-September/023761.html