[gmx-users] DMF topology

[Abhishek Banerjee]

Hi,
          After long try and error and with some reference I made a topology  of DMF with six site interaction using OPLS/AA and topolgen. Can some tell me is it the correct format of a topology file or do i need to consider any other fact.

;
;     OPLS-AA topology, built by TopolGen version 1.0 (3/21/2009)
;     Script written by: Justin Lemkul (jalemkul at vt.edu)
;     This is your molecule's topology
;     Check it carefully for any errors. It is not necessarily perfect!
;
;     Topology written on Sun Sep  6 15:41:15 IST 2009
;
; Include force field
#include "ffoplsaa.itp"
[ atomtypes ]
C3         15.03500     0.285       A    3.80000e-01  7.11280e-01
N          14.00670    -0.570       A    3.25000e-01  7.11280e-01
C          12.01100     0.500       A    3.80000e-01  4.81160e-01
H           1.00800     0.020       A    2.50000e-01  1.25520e-01
O          15.99940    -0.500       A    2.96000e-01  8.78640e-01

[ moleculetype ]
; Name            nrexcl
DMF                 3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
     1  C3      1    DMF     CM1      1       0.285   12.01100                             
     2   N      1    DMF     NM      1      -0.570   14.00670                             
     3  C3      1    DMF     CM2      1       0.285   12.01100                             
     4   C      1    DMF     CF     1        0.500   12.01100                             
     5   H      1    DMF     HF      1       0.020    1.00800                             
     6   O      1    DMF     OF      1      -0.500   15.99940                             

[ bonds ]
;  ai    aj funct
    1     2     1    0.14490        282001.6
    2     3     1    0.14490        282001.6
    2     4     1    0.13350       410032.0
    4     5     1    0.10900       284512.0
    4     6     1    0.12290       476976.0

[ pairs ]
;  ai    aj funct
    1     5     1
    1     6     1
    3     5     1
    3     6     1

[ angles ]
;  ai    aj    ak funct
    1     2     3     1        116.200    711.280
    1     2     4     1        121.900    418.400
    3     2     4     1        121.900    418.400
    2     4     5     1        109.500    292.880
    2     4     6     1        122.900    669.440
    5     4     6     1        123.000    292.880

[ dihedrals ]
;  ai    aj    ak    al funct
    1     2     4     5     3    -0.29079  -0.87237   0.00000   1.16315   0.00000   0.00000
    1     2     4     6     3    25.47638   0.00000 -25.47638   0.00000   0.00000   0.00000
    3     2     4     5     3    -0.29079  -0.87237   0.00000   1.16315   0.00000   0.00000
    3     2     4     6     3    25.47638   0.00000 -25.47638   0.00000   0.00000   0.00000

[ dihedrals ]
;  aj    ak    ai    al funct
    1     3     2     4     1    improper_Z_N_X_Y
    2     6     4     5     1    improper_O_C_X_Y

[ system ]
; Name
DMF, generated by TopolGen

[ molecules ]
; Compound        #mols
DMF                 1

Thanks
abhishek



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