[gmx-users] protein / bilayer problems

[jxs818 at bham.ac.uk]

Hi all, 
I am having a bit of trouble putting a protein into a 
bilayer. The first part, actually putting the hole in the 
bilayer went really well (Nice one Graham, for the gromacs 
3 mdrun_hole version). However, when I merge the bilayer 
and the protein gro files, amend the top file etc and do 
grompp I get the non zero system charge warning (Do I amend 
this through genion???—charge -9.98999 E-01) and the warning

Warning: atom names in rhod.top and merged.gro don't match 
(N - C1)
Warning: atom names in rhod.top and merged.gro don't match 
(H1 - C2)
Warning: atom names in rhod.top and merged.gro don't match 
(H2 - C3)
Warning: atom names in rhod.top and merged.gro don't match 
(H3 - N4)
<snip>

(more than 20 non-matching atom names)
WARNING 2 [file "rhod.top", line 22458]:
  12336 non-matching atom names
  atom names from rhod.top will be used
  atom names from merged.gro will be ingnored

I have tried changing the order of .itp files etc in 
the .top file to see if I can get rid of the ‘non matching 
atom warnings’ but when I do I get the error

 Fatal error: Invalid order for directive atomtypes, 
file ""lipid.itp"", line 11

Finally, If I ignore the warnings and carry on with a mdrun 
I get this warning

step 0Warning: 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.
<snip>

and the fatal error 

ci=-1 

Incidentally I am using the ffgmx forcefield, and when I 
try use the ffg43a forcefield I constantly get the 

Fatal error: Invalid order for directive atomtypes, 
file ""lipid.itp"", line 11

error no matter the order of the includes in the top file. 

Can anyone help or has anyone come across the same 
troubles? 

As usual any help would be gratefully received.
John  :-(