;
;	File 'topol.top' was generated
;	By user: Oda (501)
;	On host: Odas-MacBook-Pro.local
;	At date: Sat Apr 20 20:11:49 2019
;
;	This is a standalone topology file
;
;	Created by:
;	                    :-) GROMACS - gmx pdb2gmx, 2018.3 (-:
;	
;	Executable:   /usr/local/bin/../Cellar/gromacs/2018.3/bin/gmx
;	Data prefix:  /usr/local/bin/../Cellar/gromacs/2018.3
;	Working dir:  /Users/Oda/Documents/Schrodinger/Files simulation bigger box
;	Command line:
;	  gmx pdb2gmx -f AuroraB_system_no_water.pdb -o AuroraB_partP_processed.gro -water tip3p -ff charmm36-nov2018
;	Force field was read from current directory or a relative path - path added.
;

; Include forcefield parameters
#include "./charmm36-nov2018.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_D.itp"
#include "topol_Ion_chain_A2.itp"
#include "topol_Other_chain_A3.itp"

; Include water topology
#include "./charmm36-nov2018.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 "./charmm36-nov2018.ff/ions.itp"

[ system ]
; Name
Model of chainA_  based on chainA_A chainB_B in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_D     1
Ion_chain_A2        1
Other_chain_A3      1
SOL         35687
NA               104
CL               113