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"
#else
#include "spc.itp"
#endif
[ 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.
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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
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Would you tell me what files, i have to modify. Any suggestion is appreciated.
Thank you in
advance.
with regards,
Nagaraju
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