[gmx-users] ffbond.itp

[Justin Lemkul]

On 2/17/15 7:27 AM, marzieh dehghan wrote:
> Hi every body
> *in order to complete ffbond.itp for new covalent bond, we use the
> following article A Biomolecular Force Field Based on the Free Enthalpy of
> Hydration and Solvation: The GROMOS Force-Field **Parameter Sets 53A5 and
> 53A6",but we can't find out how to solve these problems?*

In the strictest sense, if you're missing bonded parameters, you have to derive 
them using some target data like QM vibrational spectra and optimized geometry. 
  In practice, you can often assign something feasible by analogy to existing 
groups (always validate!).

> *1-Gromos angle (ga_????) for "CH1-C-CH2"?*

-C- implies a planar group, so there will be something reasonably similar 
already defined.  Try those parameters to start.

> *2-How to determine "atom type" for oxygen bonded to phosphate group?*
> CH2OPO-23

Which oxygen?  They're different.  They can be either OA or OM; see 
atomtypes.atp and other relevant force field files.

> *3-Dihedrals parameters for the following cases:*
> *C CH1 O CH2*
> *CH2 OA P OM*
> *CH1 CH2 OA P *
> *CH2 CH1 OA H*
> *CH1 CH1 CH1 CH2*
> *C CH1 CH1 CH1*
>
> *CH1 CH1 C CH2*

Dihedrals are hard because they're not generally very transferable.  The second 
one is probably covered by whatever nucleic acid parameters are already in 53A6, 
but I don't know anyone that uses 53A6 to simulate nucleic acids, so I don't 
know how good the parameters are.  The rest would probably have to be 
parametrized from scratch.

-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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