[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file

[sreeta.g]

Hi Justin

I have changed all the force field parameters as below, (I have already
shown my ffbonded.itp file)
ffnonbonded.itp
; name  bond_type    mass    charge   ptype          sigma      epsilon
 opls_966   CA    6    12.01100      0.240       A    3.5000e-01  
3.3600e-01
 opls_967   CA    6    12.01100      0.180       A    3.5000e-01  
3.3600e-01
 opls_968   HB1   1    1.00800       0.060       A    2.5700e-01  
2.1000e-01
 opls_969   HB2   1    1.00800       0.060       A    2.5700e-01  
2.1000e-01
 opls_970   HB3   1    1.00800       0.060       A    2.5700e-01  
2.1000e-01
 opls_971   HA1   1    1.00800       0.060       A    2.5700e-01  
2.1000e-01
 opls_972   HA2   1    1.00800       0.060       A    2.5700e-01  
2.1000e-01

atomname2type.n2t
C    opls_136    -0.120 12.011  4    C 0.153   H 0.11    H 0.110   H 0.110
C    opls_966     0.240 12.011  4    C 0.153   H 0.11    H 0.110   O 0.143
C    opls_135    -0.180 12.011  4    C 0.153   H 0.11    H 0.110   H 0.110
O    opls_154    -0.700 15.999  2    C 0.143   H 0.097

aminoacid.rtp
[ Pva ]
  [ atoms ] ; see atomtypes.atp for explainations
    CB    opls_136     -0.120     1
    HB1   opls_968     0.060     1
    HB2   opls_969     0.060     1
    CA    opls_966     0.240     2
..... (contd)

so I have maintained consistency in my atom types in the ffbonded.itp files.
When I am running Grompp, it gives 7988 errors and I have 9088 atoms in my
polymer chain. All the errors mentioned are No default Ryckaert-Bell. types,
which I explained to you in my first mail.

So I am still unsure as to what my problem is and how I should deal with it.

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