[gmx-users] Fw: Add new residue to oplsaa force field

Wed Dec 17 09:50:48 CET 2014

Dear JustinThanks for your tip, After I edit atomtype in ffbonded file problem solved. There is a new problem. I made hydroxyprolin top file by mktop and I added bond, angle and dihedral parameters to the ffbonded file. 

;
; This topology was generated by MKTOP ;

; Please cite this work.

; Ribeiro, A.A.S.T.; Horta, B.A.C.; de Alencastro, R.B.  J. Braz. Chem. Soc., Vol. 19, No. 7, 1433-1435, 2008.

; MKTOP does not generate charges!!! You will need to take care of that yourself!!

; Check your topology!! Make sure the atom types make sense.

#include "/opt/bio/gromacs/share/gromacs/top/oplsaa.ff/forcefield.itp"

[ moleculetype ]
; Name            nrexcl
MOL             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
        1  opls_902   1   HYP      N1    5   -0.14000     14.0067   
        2  opls_135   1   HYP      C1    1   0.01000     12.011   
        3  opls_235   1   HYP      C2    2   0.50000     12.011   
        4  opls_281   1   HYP      O1    2   -0.50000     15.9994   
        5  opls_136   1   HYP      C3    3   -0.12000     12.011   
        6  opls_158   1   HYP      C4    4   -0.12000     12.011   
        7  opls_908   1   HYP      C5    5   -0.05000     12.011   
        8  opls_154   1   HYP      O2    4   -0.68300     15.9994   
        9  opls_140   1   HYP      H1    1   0.06000     1.008   
       10  opls_140   1   HYP      H2    3   0.06000     1.008   
       11  opls_140   1   HYP      H3    3   0.06000     1.008   
       12  opls_140   1   HYP      H4    4   0.06000     1.008   
       13  opls_155   1   HYP      H5    4   0.06000     1.008   
       14  opls_140   1   HYP      H6    5   0.06000     1.008   
       15  opls_140   1   HYP      H7    5   0.06000     1.008   

[ bonds ]
1 7 1   0.146  319657.6
1 2 1   0.147  319657.6
2 9 1   0.109  284512.0
2 5 1   0.154  224262.4
2 3 1   0.153  224262.4
3 4 1   0.122  200000.0
5 11 1   0.109  284512.0
5 10 1   0.109  284512.0
5 6 1   0.150  224262.4
6 12 1   0.109  284512.0
6 8 1   0.141  267776.0
6 7 1   0.151  224262.4
7 15 1   0.109  284512.0
7 14 1   0.109  284512.0
8 13 1   0.096  462750.4

[ angles ]
1 7 6 1  103.026  470.281
1 7 15 1  113.597  292.880
1 7 14 1  109.458  292.880
1 2 9 1  114.712  292.880
1 2 5 1  103.936  470.281
1 2 3 1  108.272  669.440
2 1 7 1  110.799  433.462
2 5 11 1  113.386  313.800
2 5 10 1  109.493  313.800
2 5 6 1  103.337  488.273
2 3 4 1  120.399  200.000
3 2 9 1  106.795  418.400
3 2 5 1  112.252  585.760
5 2 9 1  110.968  313.800
5 6 12 1  113.836  313.800
5 6 8 1  108.872  418.400
5 6 7 1  103.268  488.273
6 5 11 1  113.403  313.800
6 5 10 1  109.458  313.800
6 8 13 1  109.466  460.240
6 7 15 1  113.577  313.800
6 7 14 1  109.490  313.800
7 6 12 1  113.170  313.800
7 6 8 1  109.597  418.400
8 6 12 1  107.964  292.880
10 5 11 1  107.676  276.144
14 7 15 1  107.597  276.144

[ dihedrals ]
2 1 7 6 3
2 1 7 15 3
2 1 7 14 3
7 1 2 9 3
7 1 2 5 3
7 1 2 3 3
1 2 5 11 3
9 2 5 11 3
3 2 5 11 3
1 2 5 10 3
9 2 5 10 3
3 2 5 10 3
1 2 5 6 3
9 2 5 6 3
3 2 5 6 3
1 2 3 4 3
9 2 3 4 3
5 2 3 4 3
2 5 6 12 3
11 5 6 12 3
10 5 6 12 3
2 5 6 8 3
11 5 6 8 3
10 5 6 8 3
2 5 6 7 3
11 5 6 7 3
10 5 6 7 3
5 6 8 13 3
12 6 8 13 3
7 6 8 13 3
5 6 7 1 3
12 6 7 1 3
8 6 7 1 3
5 6 7 15 3
12 6 7 15 3
8 6 7 15 3
5 6 7 14 3
12 6 7 14 3
8 6 7 14 3

[ dihedrals ]

[ pairs ]
6 2 1
15 2 1
14 2 1
9 7 1
5 7 1
3 7 1
11 1 1
11 9 1
11 3 1
10 1 1
10 9 1
10 3 1
6 1 1
6 9 1
6 3 1
4 1 1
4 9 1
4 5 1
12 2 1
12 11 1
12 10 1
8 2 1
8 11 1
8 10 1
7 2 1
7 11 1
7 10 1
13 5 1
13 12 1
13 7 1
1 5 1
1 12 1
1 8 1
15 5 1
15 12 1
15 8 1
14 5 1
14 12 1
14 8 1

[ system ]
; Name
MKTOP

[ molecules ]
; Compound        #mols
MOL             1 
As you can see in the topology file from mktop, there is no dihedral coefficients in the proper dihedral section that leads to creation of new error after grompp command. Why mktop doesn't produce these dihedral coefficient? and how can I solve it?Thanks in advance

Fatemeh Ramezani