[gmx-users] Need to confirm parameters.

[Justin Lemkul]

On 5/19/17 8:22 AM, Sailesh Bataju wrote:
> Hi Sir,
>
> You mean like choosing OPLS forcefield for all-atom model would be moer
> appropriate for me?
>

At minimum, some all-atom force field, because whatever you were doing before 
has no relationship to GROMOS and is unlikely to succeed.

Isobutane is just the valine side chain, so that's certainly a model compound in 
existing force fields and should have parameters published and validated for any 
of the major all-atom force fields.  I know it's in CHARMM, and certainly others.

-Justin

> Thank you.
>
> On Fri, May 19, 2017 at 5:15 PM, Sailesh Bataju <thelaven at gmail.com> 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.
>>
>> I need your advice to help me decide to go further.
>> Thank you very much.
>>
>> --
>> Self-reliant is the great potential for success.
>>
>
>
>

-- 
==================================================

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

==================================================