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 <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

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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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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