[gmx-users] Regarding engineered residue topology

[Venkat Reddy]

Thank you Justin for clear explanation.
However, the parameters are available for
CX     CT     CT_2   HC      3      0.96650   2.89951   0.00000  -3.86601
0.000   0.000;
C*     CT     CT_2   HC      3      0.96650   2.89951   0.00000  -3.86601
0.000   0.000 ;
So, can I apply the same for CT-CT_2-CT-HC dihedral?

Thank you for your valuable time and concern.

On Mon, Jul 27, 2015 at 5:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/27/15 1:21 AM, Venkat Reddy wrote:
>
>> 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?
>>
>>
> You're confusing atom names and atom types.  The names are totally
> irrelevant for parameter assignment.  The CB2-C1-CB1-HB11 dihedral has a
> sequence of nonbonded types of opls_135-opls_225B-opls_135-opls_140, which
> have bonded types (see second column of ffnonbonded.itp) of CT-CT_2-CT-HC.
> So the parameters you need are for CT-CT_2-CT-HC, which are indeed not in
> ffbonded.itp.
>
> -Justin
>
>
>  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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>>
>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036