[gmx-users] grompp error in simulation of membrane protein.

[nitu sharma]

Hello justin ,

thanks for ur previous suggestion . I am doing simulation of membrene
protein  , as u suggest in  previous mail to use gromos9653a6 forcefield
parameters  in topology file of protein+lipid bilayer.
I have made topology accordingly like this-

; Include forcefield parameters
#include "ffG53a6.itp"
#include "lipid.itp"
#include "dmpc.itp"

; Include chain topologies
#include "rr1_A.itp"
#include "rr1_B.itp"

; Include position restrain protein
;#ifdef POSRES_PROTEIN
;#include "posre_A.itp"
;#include "posre_B.itp"
;#endif

; Include position restrain lipid
;#ifdef POSRES_LIPID
;#include "lip_posre.itp
;#endif

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

#ifdef POSRES_WATER
;Position restraint for each water oxygen
[ position_restraints ]
; i funct  fcx      fcy      fcz
  1  1     1000     1000     1000
#endif

; Include generic topology for ions
#include "ions.itp"


[ system ]
; Name
PROTEIN IN DMPC BILAYER + WATER

[ molecules ]
; compound  #mols
Protein_A    1
Protein_B    1
DMPC        128
SOL        3552
Na           1

But when I run the grompp command I got the error like this-
Fatal error:
Atomtype CA not found

I have tried to solve this problem by adding CA atom with its mass  in
ffG53a6.atp file and atom CA with its all information ffG53a6nb.itp file but
even after doing this correction I am getting same error .
Please Can u suggest me what should I have to do to solve this problem .

I am a new gromacs user , I have done the simulation of protein and lipid
bilayer separetly but this type of problem didnot came so I have no much
idea .
I am waiting for ur reply.

NITU SHARMA
SCHOOL OF LIFE SCIENCES
JAWAHERLAL NEHRU UNIVERSITY
NEW DELHI, INDIA
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