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

[Justin Lemkul]

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.
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