[gmx-users] Diagnosing + system blowing up

[Mark Abraham]

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