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

Justin Lemkul jalemkul at vt.edu
Thu Oct 26 13:08:04 CEST 2017

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?


Sounds like you forgot step 5.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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