[gmx-users] Unknown bond_atomtype CAY

[Sameer Edirisinghe]

Dear Dr. Justin,

Thanks for the explanation. Now i got the point you mentioned here. Then i
checked the bonds i have mentioned in .rtp file and then i found the
relevant bonded type. then i checked the ffbonded.itp file and i found that
bond type is already in there.
As an example,

CAY  HA1 ; this is one of bond i have in .rtp file. and for that bond,
relevant bond type (mentioned as below) was already in ffbonded.itp file
CT    HC      1    0.10900   284512.0

But still following error is occurring while running 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

How do i refer particular bond types in ffbonded.itp file to my current
.gro file or any other relevant file ?

regards

On Tue, Sep 20, 2016 at 9:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/20/16 8:27 AM, Sameer Edirisinghe wrote:
>
>> 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.
>>
>>
> Look at ffnonbonded.itp.  The first column is the opls_* type.  The second
> column is the corresponding bonded type.  The bonded types are what you use.
>
> 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 ) ?
>>
>>
> These are the types listed in the second column of ffnonbonded.itp.
>
> 3) Do i need to define bonds in and atom in .rtp file and .pdb file using
>> above nomenclature/type ?
>>
>>
> The .rtp names must match the PDB atom names.  The [atoms] section of an
> .rtp entry defines a given atom's name, type, charge, and charge group.
> All remaining bonded interactions in an .rtp entry are defined using name
> only.
>
> -Justin
>
>
> Regards
>>
>>
>>
>> On Tue, Sep 20, 2016 at 12:59 AM, Justin Lemkul <jalemkul at 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
>>>
>>> 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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