[gmx-users] Lipid bilayer parameters

[naga raju]

Dear gmx-users,
                I built a lipid bilayer (72 lipid
molecules and 2376 water molecules) by taking one
lipid molecule from the dppc.pdb file in website:
http://moose.bio.ucalgary.ca/index.php?page=Downloads
 I downloaded dppc.itp and lipid.itp files from the
above link. when i used the grompp command, it shows
the following error. 

Warning: atom names in dppc.top and bbww.pdb don't
match (C1 - C2)
Warning: atom names in dppc.top and bbww.pdb don't
match (C2 - N4)
Warning: atom names in dppc.top and bbww.pdb don't
match (N4 - C5)
Warning: atom names in dppc.top and bbww.pdb don't
match (C5 - C6)
Warning: atom names in dppc.top and bbww.pdb don't
match (C6 - O7)
Warning: atom names in dppc.top and bbww.pdb don't
match (O7 - P8)
Warning: atom names in dppc.top and bbww.pdb don't
match (P8 - O9)
Warning: atom names in dppc.top and bbww.pdb don't
match (O9 - O10)
Warning: atom names in dppc.top and bbww.pdb don't
match (O10 - O11)
Warning: atom names in dppc.top and bbww.pdb don't
match (O11 - C12)
Warning: atom names in dppc.top and bbww.pdb don't
match (C12 - C13)
Warning: atom names in dppc.top and bbww.pdb don't
match (C13 - O14)
Warning: atom names in dppc.top and bbww.pdb don't
match (O14 - C15)
Warning: atom names in dppc.top and bbww.pdb don't
match (C15 - O16)
Warning: atom names in dppc.top and bbww.pdb don't
match (O16 - C17)
Warning: atom names in dppc.top and bbww.pdb don't
match (C17 - C18)
Warning: atom names in dppc.top and bbww.pdb don't
match (C18 - C19)
Warning: atom names in dppc.top and bbww.pdb don't
match (C19 - C20)
Warning: atom names in dppc.top and bbww.pdb don't
match (C20 - C21)
Warning: atom names in dppc.top and bbww.pdb don't
match (C21 - C22)
(more than 20 non-matching atom names)
WARNING 1 [file "dppc.top", line 26]:
  9096 non-matching atom names
  atom names from dppc.top will be used
  atom names from bbww.pdb will be ingnored
 
double-checking input for internal consistency...
ERROR: One of the box vectors is shorter than twice
the cut-off length. Increase the box size or decrease
rlist.
There was 1 warning


How can be the problem solved?
Here i gave my dppc.top file:

#include "ffgmx.itp"
#include "lipid.itp"
#include "dppc.itp"
#include "alm.itp"
#include "ions.itp"

#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
Alm on surf + relaxed popc

[ molecules ]
; name	number
DPPC    72
SOL     2376


                 Thank you
                                  nagaraju



		
____________________________________________________
Start your day with Yahoo! - make it your home page 
http://www.yahoo.com/r/hs