bnz.top

;
;	File '6lyz_gmx.top' was generated
;	By user: sunhwan (40816)
;	On host: kuta
;	At date: Fri Nov 10 13:02:26 2017
;
;	This is a standalone topology file
;
;	Created by:
;	           :-) GROMACS - gmx pdb2gmx, 2017-dev-20170822-762c6f0 (-:
;	
;	Executable:   /home/sunhwan/local/gromacs/src/gromacs/build/bin/gmx
;	Data prefix:  /home/sunhwan/local/gromacs/src/gromacs (source tree)
;	Working dir:  /data/sunhwan/work/lysozyme/1_setup
;	Command line:
;	  gmx pdb2gmx -f 6lyz_4pdb2gmx.pdb -o 6lyz_gmx.pdb -p 6lyz_gmx.top -ff charmm36 -water tip3p -ter -merge all
;	Force field was read from current directory or a relative path - path added.
;

[ defaults ]
; nbfunc	comb-rule	gen-pairs	fudgeLJ	fudgeQQ
1	2	yes	1.0	1.0

[ atomtypes ]
;type atnum         mass   charge  ?           sigma  epsilon
CG2R61    6    12.011000    0.000  A  0.355005321205  0.29288
HGR61     1     1.008000    0.000  A  0.242003727796  0.12552
LP        0     0.000000    0.00   A  0.0             0.0    ; pram

[ bondtypes ]
;      i        j  func           b0           kb
  CG2R61   CG2R61     1   0.13750000    255224.00
  CG2R61    HGR61     1   0.10800000    284512.00

[ angletypes ]
;      i        j        k  func       theta0       ktheta          ub0          kub
  CG2R61   CG2R61   CG2R61     5   120.000000   334.720000   0.24162000     29288.00
  CG2R61   CG2R61    HGR61     5   120.000000   251.040000   0.21525000     18409.60

[ dihedraltypes ]
;      i        j        k        l  func         phi0         kphi  mult
  CG2R61   CG2R61   CG2R61   CG2R61     9   180.000000    12.970400     2
  CG2R61   CG2R61   CG2R61    HGR61     9   180.000000    17.572800     2
   HGR61   CG2R61   CG2R61    HGR61     9   180.000000    10.041600     2

[ dihedraltypes ]
; 'improper' dihedrals 
;      i        j        k        l  func         phi0         kphi

[ moleculetype ]
; Name            nrexcl
BENX              3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
; residue   1 BENX rtp BENX q  0.0
     1     CG2R61      1   BENX     CG      1     -0.115     12.011   ; qtot -0.115
     2      HGR61      1   BENX     HG      1      0.115      1.008   ; qtot 0
     3     CG2R61      1   BENX    CD1      1     -0.115     12.011   ; qtot -0.115
     4      HGR61      1   BENX    HD1      1      0.115      1.008   ; qtot 0
     5     CG2R61      1   BENX    CD2      1     -0.115     12.011   ; qtot -0.115
     6      HGR61      1   BENX    HD2      1      0.115      1.008   ; qtot 0
     7     CG2R61      1   BENX    CE1      1     -0.115     12.011   ; qtot -0.115
     8      HGR61      1   BENX    HE1      1      0.115      1.008   ; qtot 0
     9     CG2R61      1   BENX    CE2      1     -0.115     12.011   ; qtot -0.115
    10      HGR61      1   BENX    HE2      1      0.115      1.008   ; qtot 0
    11     CG2R61      1   BENX     CZ      1     -0.115     12.011   ; qtot -0.115
    12      HGR61      1   BENX     HZ      1      0.115      1.008   ; qtot 0
    13         LP      1   BENX    LPA      1      0.000      0.000   ; qtot 0

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1 
    1     3     1 
    1     5     1 
    3     4     1 
    3     7     1 
    5     6     1 
    5     9     1 
    7     8     1 
    7    11     1 
    9    10     1 
    9    11     1 
   11    12     1 

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     8     1 
    1    10     1 
    1    11     1 
    2     4     1 
    2     6     1 
    2     7     1 
    2     9     1 
    3     6     1 
    3     9     1 
    3    12     1 
    4     5     1 
    4     8     1 
    4    11     1 
    5     7     1 
    5    12     1 
    6    10     1 
    6    11     1 
    7    10     1 
    8     9     1 
    8    12     1 
   10    12     1 

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     3     5 
    2     1     5     5 
    3     1     5     5 
    1     3     4     5 
    1     3     7     5 
    4     3     7     5 
    1     5     6     5 
    1     5     9     5 
    6     5     9     5 
    3     7     8     5 
    3     7    11     5 
    8     7    11     5 
    5     9    10     5 
    5     9    11     5 
   10     9    11     5 
    7    11     9     5 
    7    11    12     5 
    9    11    12     5 

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    2     1     3     4     9 
    2     1     3     7     9 
    5     1     3     4     9 
    5     1     3     7     9 
    2     1     5     6     9 
    2     1     5     9     9 
    3     1     5     6     9 
    3     1     5     9     9 
    1     3     7     8     9 
    1     3     7    11     9 
    4     3     7     8     9 
    4     3     7    11     9 
    1     5     9    10     9 
    1     5     9    11     9 
    6     5     9    10     9 
    6     5     9    11     9 
    3     7    11     9     9 
    3     7    11    12     9 
    8     7    11     9     9 
    8     7    11    12     9 
    5     9    11     7     9 
    5     9    11    12     9 
   10     9    11     7     9 
   10     9    11    12     9 


[ virtual_sites2 ]
; Vsite from                    funct   a 
13       1       11       1      0.500

[ atomtypes ]
;type atnum         mass   charge  ?           sigma  epsilon
; special dummy-type particles
LP      0       0.000000        0.00    A       0.0     0.0    ; pram

; NBFIX for LP, rmin=1.2/2^(1/6), eps=4.184*.01
[ nonbond_params ]
LP     LP  1  1.069078461768  0.041840000000                 ; pram

[ system ]
; Name
two benzene

[ molecules ]
; Compound        #mols
BENX     2