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