[gmx-users] Re: Urea-Gromos96

[Alessandra Villa]

> 	Hi Gromacs users,
> Does anybody have Gromos96 topology file of Urea?
>
> Thanks
> Jozef
>
>
>

If you mean the urea model of Smith,
this should be the topologies.
please check before using it.

Alessandra


*********
;	O			02
;	|			|
;	C			C1
;      / \		       / \ 
; H11-N1  N2-H21           H4-N3  N6-H7
;      |  |		      |   |
;    H12  H22		     H5   H8 
; 
[ moleculetype ]
; name  nrexcl
Urea         3

[ atoms ]
;   nr    type   resnr  residu    atom    cgnr  charge  mass
      1    CUREA      1    UREA      C1       1	 0.142	12.01100
      2    OUREA      1    UREA      O2       1	-0.390  15.99940
      3    NUREA      1    UREA      N3       2	-0.542  14.00670
      4       H       1    UREA      H4       2	 0.333   1.00800
      5       H       1    UREA      H5       2	 0.333   1.00800
      6    NUREA      1    UREA      N6       3	-0.542  14.00670
      7       H       1    UREA      H7       3   0.333   1.00800
      8       H       1    UREA      H8       3	 0.333   1.00800


[ bonds ]
;  ai    aj funct           bo           Kb
     3     4     2 1.000000e-01 18.7e+06
     3     5     2 1.000000e-01 18.7e+06
     6     7     2 1.000000e-01 18.7e+06
     6     8     2 1.000000e-01 18.7e+06
     1     2     2 1.265000e-01 13.1e+06
     1     3     2 1.350000e-01 10.3e+06
     1     6     2 1.350000e-01 10.3e+06

[ pairs ]
;  ai    aj funct             c0           c1
     2     4     1   0.000000e+00 0.000000e+00
     2     5     1   0.000000e+00 0.000000e+00
     2     7     1   0.000000e+00 0.000000e+00
     2     8     1   0.000000e+00 0.000000e+00
     3     7     1   0.000000e+00 0.000000e+00
     3     8     1   0.000000e+00 0.000000e+00
     4     6     1   0.000000e+00 0.000000e+00
     5     6     1   0.000000e+00 0.000000e+00

[ angles ]
;  ai    aj    ak funct     Theta0       K
     1     3     4     2  1.200000e+02 3.9000e+02
     1     3     5     2  1.200000e+02 3.9000e+02
     4     3     5     2  1.200000e+02 4.4500e+02
     1     6     7     2  1.200000e+02 3.9000e+02
     1     6     8     2  1.200000e+02 3.9000e+02
     7     6     8     2  1.200000e+02 4.4500e+02
     2     1     3     2  1.214000e+02 6.9000e+02
     2     1     6     2  1.214000e+02 6.9000e+02
     3     1     6     2  1.172000e+02 6.3600e+02

[ dihedrals ]
;improper dihedrals, planar groups
;  ai    aj    ak    al funct     Angle0        K
     1     3     6     2     2	  0.00	      0.0510 ;gi_1
     3     4     5     1     2     0.00        0.0510 ;gi_1
     6     7     8     1     2     0.00        0.0510 ;gi_1

[ dihedrals ]
;torsional (proper) dihedral
;  ai    aj    ak    al funct   Angle              K   M
    2     1     3     4     1    180.00           41.8  2
    2     1     6     7     1    180.00           41.8  2