Dear Dr. Justin,

Thanks for the all valuable points here. Please see the below sample bonds
i defined in .rtp file. how to define bond type for them ? i know oplsaa
atom type of each of them. what i dont understand in how to add them to
ffbonded.itp file. these bonds are general bonds such as C-C , C-H C-O
bonds. 1) I dont understand how to define them in ffbonded.itp file.

2) what is the nomenclature/type which used in  ffbonded.itp file  to
define atoms (i.e. OW    HW , OW    LP, C_2   C3 , C     CA ) ?

3) Do i need to define bonds in and atom in .rtp file and .pdb file using
above nomenclature/type ?

Regards



On Tue, Sep 20, 2016 at 12:59 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 9/18/16 10:14 PM, Sameer Edirisinghe wrote:
>
>> Dear Dr. Justin,
>>
>> If the bond types have not added, following errors occuring with grompp,
>>
>> 1) ERROR 1 [file topol.top, line 108]:
>>   No default Bond types
>>
>> 2) ERROR 2 [file topol.top, line 168]:
>>   No default Angle types
>>
>> 3) ERROR 3 [file topol.top, line 426]:
>>   No default Ryckaert-Bell. types
>>
>> Atom types are seems to be correct as i derived them from atomtype.atp
>> file.
>>
>> If the interaction don't cover by the force field, how can I define them
>> in
>> ffbonded.itp file ?
>>
>>
> See the manual.  Use atom types, not names.  If you're adding parameters,
> be sure they've been derived properly.  If you're still using anything from
> that PRODRG topology and trying to force it into OPLS-AA, don't.
>
> -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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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