[gmx-users] SwissParam itp files

[Justin Lemkul]

On 6/8/15 10:30 AM, soumadwip ghosh wrote:
> Hi Justin and Albert
>
> Thanks for your help. In order to reply Justin's comment I would like to
> say that there are numerous examples of such kinds of fullerene-organic
> binder interaction.
>
> http://www.sciencedirect.com/science/article/pii/S0045653513001215#
>
> If you look at the above paper, t deals with the adsorption of many such
> binders on the surface of simple buckyballs via on-covalent interactions.
> They took almost 5 mols of binder/ fullerene and there are even reports
> where aggregates of fullerene assembly has been shown to bind strongly with
> organic binders in water.
> http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp41117b?page=search
>
>   I am wondering why it ain't working with my set up of force field and a
> topology built from a web source. At present , i am thinking of getting
> started with 1:1 combination of fullerene and binder and try to reproduce
> the above work, then probably optimize the assembly in terms of its
> physical properties such as solvation and others. I would love to have an
> opinion on it.
>

Reproducing what you know should work is a wise first step.  Otherwise, you're 
working in the dark if you don't have any idea if your particular molecule 
should associate in some way.  If you're simply testing whether or not this 
particular molecule binds, well then you have your answer, at least in the 
context of a model of yet-to-be-determined accuracy.  Start with something you know.

>
> I dint know about the appropriateness of SwissParam. In this case do I
> really need to switch to CGenFF ?
>

I strongly recommend using ParamChem to generate CGenFF topologies.  It provides 
penalty scores so you know (1) how reasonable the topology is and (2) exactly 
what may need refinement.  Most other servers are black boxes; you have to cross 
your fingers and hope they work.  CGenFF coverage of chemical space is quite 
good, unless you have something really bizarre.

-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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