[gmx-users] Urea Topology

[Sagar De'Biomimic]

Dear Gromacs user,
I have been trying to make correct topology for Urea. We have some
simulations planned for 9M urea.
I could make the following topology based on Smith et al and would like to
know if i am wrong somewhere.

[ moleculetype ]
; molname    nrexcl
URE        3

[ atoms ]
     1  C            1  URE      C      1     0.142  12.01000  69.906E-03
3.6864E-03     ; amber C  type
     2  O            1  URE     O      2    -0.390  16.00000  48.620E-03
1.2609E-03     ; amber O  type
     3  N            1  URE     N1      3    -0.542  14.01000  57.903E-03
1.9877E-03     ; amber N  type
     4  H            1  URE    H11      4     0.333   1.00800  0.0
0.0            ; amber H  type
     5  H            1  URE    H12      5     0.333   1.00800  0.0
0.0            ; amber H  type
     6  N            1  URE     N2      6    -0.542  14.01000  57.903E-03
1.9877E-03     ; amber N  type
     7  H            1  URE    H21      7     0.333   1.00800  0.0
0.0            ; amber H  type
     8  H            1  URE    H22      8     0.333   1.00800  0.0
0.0            ; amber H  type

[ bonds ]
    1    2    2    0.1265    13.1
    1    3    2    0.135    10.3
    1   6    2    0.135    10.3
    3    4    2    0.100    18.7
    3    5    2    0.100    18.7
    6    7    2    0.100    18.7
    6    8    2    0.100    18.7

[ angles ]
;  ai    aj    ak funct           c0           c1
    1     3     4     2 120.0 390
    1     3     5     2 120.0 390
    4     3     5     2 120.0 445
    1     6     7     2 120.0 390
    1     6     8     2 120.0 390
    7     6     8     2 120.0 445
    2     1     3     2 121.4 690
    2     1     6     2 121.4 690
    3     1     6     2 117.2 636
[ dihedrals ]
;   ai    aj    ak    al funct  definition
     2     1     3     4   9    180.0 41.8 2
     2     1     6     7   9    180.0 41.8 2

[ dihedrals ]
     3     6     1     2   2    0.0 167.42
     1     4     3     5   2    0.0 167.42
     1     7     6     8   2    0.0 167.42


If it is right I would also like it to be available for all users.

Thank you.
Regards

-- 
Sagar Khavnekar
Project student,
Structural Biology and Molecular Biophysics lab,
UM-DAE Centre for Excellence in Basic Sciences
University of Mumbai, Vidyanagari Campus, Kalina, Santacruz (East)
Mumbai 400098, India.