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

[Justin A. Lemkul]

On 6/29/12 6:10 PM, sreeta.g wrote:
> 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.
>

The only way to diagnose the problem is to check your self-consistency. 
Probably most of the errors are redundant.  Choose one of them (it tells you the 
line where the error occurs), write down the atom numbers involved and then look 
up which atom types (not names) to which these numbers pertain.  That is the 
missing interaction type that needs to be defined in ffbonded.itp.

I can't tell what's wrong based on the snippets of files shown.  You can, based 
on having a very careful look through all of your files.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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