[gmx-users] Need to confirm parameters.

[Justin Lemkul]

On 5/19/17 7:30 AM, Sailesh Bataju wrote:
> Hi Sir/Ma'am,
>
> I've finally created parameter file of isobutane using gromos54a7
> forcefield for all-atom model. Some of the parameters for bond angle
> parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
> file in the relevant forcefield, instead I used FTFE  -  CTFE  -  FTFE and
> CLChl  - CChl  - CLChl respectively which i found it in the sample of the
> file generated by https://atb.uq.edu.au/ website. Somehow luckily found
> corresponding bond angle approximately equivalent to the experimental data
> observed but didn't find the bond angle constant in experimental data.
> Therefore I'm not sure if I can trust the parameter selected.
>

GROMOS force fields are united-atom so isobutane will have no H atoms.  Use a 
sensible all-atom model as your starting point, because any of them will have 
the actual parameters you need rather than trying to rely on halogens as analogs 
of H atoms.

-Justin

-- 
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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

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