[gmx-users] problems in grompp

Alok Jain alokjain at iitk.ac.in
Sat Sep 11 03:02:20 CEST 2004

Thanks for ur suggestion :-)

but now i am facing new problem :-(
when i try to run grompp program i am getting following error.
Fatal error: number of coordinates in coordinate file (dppc128.gro, 11296)
             does not match topology (dppc128.top, 17365)

before  this  i made the dppc128.top file, by using bffgmx_lipids.tar.gzy 
force field  which is as  follows:-

; topology for a pure DPPC bilayer with 128 lipids and 3655 SPC water ;
#include "/root/dppc/ffgmx.itp"
;#include "lipid.itp"
#include "/root/dppc/dppc.itp"

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

[ system ]
; name
Pure DPPC bilayer with 128 lipids and 3655 water molecules

[ molecules ]
; name	number
DPPC    128
SOL     3655

After that i generate the .gro file by using editconfo program :-
editconf -f dppc128.pdb -o dppc128.gro
which contain
11296 atoms (Pure DPPC bilayer with 128 lipids and 3655 water molecules)

 plz tell me wht  can i do , to overcome that error.

> Hi Alok,
>                 You need to add new topologies at ff???.rtp file, add
> the name of your residue at aminoacid.dat file and save it in a folder
with all changed files. **(((Follow the HEME example present at
> ffgmx.rtp file)))**.
> --
>                       Arlan da Silva Gonçalves
>                IME(Instituto Militar de Engenharia)
>                 Departamento de Engenharia Química
>                  Pça. General Tibúrcio, 80 - Urca
>                  22290-270 - Rio de Janeiro - RJ
>                       Tel. (0xx21) 2546-7057
>                       Fax. (0xx21) 2546-7059
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