[gmx-users] Unknown bond_atomtype CAY
jalemkul at vt.edu
Tue Sep 20 17:58:52 CEST 2016
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.
> 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
>>> If the interaction don't cover by the force field, how can I define them
>>> 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 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
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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
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