[gmx-users] grompp error in simulation of membrane protein.
sharmanitu35 at gmail.com
Tue Apr 7 11:37:05 CEST 2009
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 chain topologies
; Include position restrain protein
; Include position restrain lipid
; Include water topology
;Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
; Include generic topology for ions
[ system ]
PROTEIN IN DMPC BILAYER + WATER
[ molecules ]
; compound #mols
But when I run the grompp command I got the error like this-
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
I am waiting for ur reply.
SCHOOL OF LIFE SCIENCES
JAWAHERLAL NEHRU UNIVERSITY
NEW DELHI, INDIA
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