;
;	File 'system.top' was generated
;	By user: jonathan (1000)
;	On host: jonathan-desktop
;	At date: Sat Jan 10 14:28:21 2015
;
;	This is a standalone topology file
;
;	It was generated using program:
;	pdb2gmx - VERSION 4.5.5
;
;	Command line was:
;	pdb2gmx -ff amber99sb -f protein.pdb -o avidin.pdb -p system.top -water tip3p -ignh 
;
;	Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"

; Include biotin_GMX.itp topology
#include "biotin_GMX.itp"

; Include chain topologies
#include "system_Protein_chain_A.itp"
#include "system_Protein_chain_B.itp"
#include "system_Protein_chain_C.itp"
#include "system_Protein_chain_D.itp"

; Include water topology
#include "amber99sb.ff/tip3p.itp"

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

; Include topology for ions
#include "amber99sb.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_B     1
Protein_chain_C     1
Protein_chain_D     1
SOL             15568
biotin             10