[gmx-users] Regarding engineered residue topology

[Venkat Reddy]

Dear Justin,
Thank you for the prompt reply. I have checked the topology file once again
and confirmed the dihedral (CB2-CA-CB1-HB11) thats creating problem. The
Aib parameters are indeed available for OPLS-AA ff. But I couldn't locate
the dihedral parameters for the above mentioned dihedral angle in
ffbonded.itp file. However I found dihedral parameters for X-CA-CB-X. So,
can I use X-CA-CB-X parameters for CB2-CA-CB1-HB11 dihedral?

On Mon, Jul 27, 2015 at 5:46 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036