[gmx-users] Regarding engineered residue topology

[Justin Lemkul]

On 7/24/15 9:20 AM, Venkat Reddy wrote:
> Dear all,
> I am trying to simulate a peptide with engineered residues like Aib (alpha
> amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though
> everything went well initially during topology generation, grompp showed
> the following error.
>
> ERROR 1 [file topol.top, line 2316]:
>    No default Ryckaert-Bell. types
> ERROR 2 [file topol.top, line 2317]:
>    No default Ryckaert-Bell. types
> ERROR 3 [file topol.top, line 2318]:
>    No default Ryckaert-Bell. types
> ERROR 4 [file topol.top, line 2325]:
>    No default Ryckaert-Bell. types
> ERROR 5 [file topol.top, line 2326]:
>    No default Ryckaert-Bell. types
> ERROR 6 [file topol.top, line 2327]:
>    No default Ryckaert-Bell. types
>
> The cross-check with topolo.top identified the dihedral CB2-CA-CB1-HB11 is
> throwing the error. My question is, even though the parameters for Aib are
> available in OPLS ff, why I am getting this error?
>

grompp doesn't lie.  Either you're looking at the wrong lines or you're looking 
at the wrong parameters.  Some residues are constructed for convenience but if 
they're not "official" then there may be problems.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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