[gmx-users] Regarding Na ions

naga raju nagaraju_cy at yahoo.co.in
Thu Jul 5 16:22:27 CEST 2007

Dear gmx users,
                                  I am trying to neutralize lipid bilayer  with Na ions by using genion command:
 genion -f bilayer.tpr -o bilayer-Na.pdb  -np  32 -pname Na  -pq 1

Here is my bilayer.top file
#include "ffoplsaa.itp"
#include "pope.itp"
#include "dpopg.itp"
#include "ions.itp"

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

[ system ]
; name
Mixture of  POPE and POPG lipid bilayer in 3:1 ratio 

[ molecules ]
; name    number
POPE      96
DPOP      32
SOL      3909
Na           32

I am getiing fallowing eror.
processing topology...
Generated 344865 of the 344865 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 344775 of the 344865 1-4 parameter combinations
Excluding 3 bonded neighbours for POPE 96
turning all bonds into constraints...
Excluding 3 bonded neighbours for DPOP 32
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 3909
turning all bonds into constraints...
Cleaning up temporary file gromppVHJgxO
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 1293
Fatal error:
No such moleculetype Na

Would you tell me what files,  i have to modify. Any suggestion is appreciated.

                                                             Thank you in advance.

                                                                                                               with regards,

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