On 30/07/2012 7:41 PM, Shima Arasteh wrote:

  You are right, CT1 is incorrect for sure. But the other option is C(carbonyl 
C) . Maybe I couldn't say it clearly.
The FVAL which I sent before through mailing list, is the result of this 
formamide and the CGenff generation:
[ FVAL ]
      [ atoms ]
         CN    C    0.357    0
         ON    O    -0.51    1
         H1    HA    0.100    2
         N    NH1    -0.423    3
         HN    H    0.333    4
         CA    CT1    0.034    5
         HA    HB    0.09    6
         CB    CT1    -0.093    7
         HB    HA    0.09    8
         CG1    CT3    -0.268    9
         HG11    HA    0.09    10
         HG12    HA    0.09    11
         HG13    HA    0.09    12
         CG2    CT3    -0.268    13
         HG21    HA    0.09    14
         HG22    HA    0.09    15
         HG23    HA    0.09    16
         C    C    0.528    17
         O    O    -0.510    18
      [ bonds ]
         CN    H1
         CN    ON
         CN    N
         N    H
         CA    N
         CA    HA
         CA    C
         C    O
         CA    CB
         CB    HB
         CB    CG1
         CB    CG2
         CG2    HG21
         CG2    HG22
         CG2    HG23
         CG1    HG11
         CG1    HG12
         CG1    HG13
[ impropers ]
       CN     N    ON    H1
This is the new residue which I defined and sent you(as remember), I used these 
parameters and atomtypes , and then went through mailing list and asked for 
your help a few days ago.
All over , with this procedure , I couldn't get the an acceptable result.

You say you've chosen suitable atom types. grompp says it can't find parameters for interactions using them. So until you find out further information, you don't have suitable atom types. I've said all I have to say until you go and look up whether the bonds, angles and dihedrals that you want to use are defined in your force field for the atom types you want to use.

If you want further help, you will need to paste your .rtp entry(s), the N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full pdb2gmx output, the N-terminal fragment of the grompp -c input, grompp command line, and full grompp output. You may think your context is clear, but nobody else is paying your problem as much attention as you are. I won't help further if you only provide partial information.

Mark
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