[gmx-users] Yet another "Fatal error: Unknown bond_atomtype" topic

[Elisa Pieri]

Damn, you're absolutely right..Thank you very very much! Now it is working.
We were using something done by others many years ago, we believed it was
fine (big mistake).

Thank you again!

On Thu, Oct 26, 2017 at 1:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/26/17 7:05 AM, Elisa Pieri wrote:
>
>> Thank you very much for the answers! We made the modifications you
>> suggested and now the error changed.
>>
>> Now we have this problem: we have an ALA residue, linked to a LYS. The LYS
>> is linked to a retinal moiety; for this, we created a "new" residue called
>> "RET" which includes LYS+retinal. But now, Gromacs is seeing the ALA as a
>> terminal residue and is adding an oxygen, witouh making the the link
>> between ALA and RET. I suppose we have to add some parameters, but we
>> couldn't really figure out which ones. Could you help us?
>>
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_
> Residue_to_a_Force_Field#Adding_a_new_residue
>
> Sounds like you forgot step 5.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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