[gmx-users] OPLS-AA forcefield parameters

[Justin A. Lemkul]

Jacob Harvey wrote:
> Dear All,
> 
> I am trying to use the OPLS-AA force field to model some imidazole 
> containing compounds. I've noticed that imidazole units are referenced 
> in the ffoplsaa.atp file as the following:
> 
> opls_557   14.00670  ; N1  in imidazole
>  opls_558   12.01100  ; C2  in imidazole
>  opls_559   14.00670  ; N3  in imidazole
>  opls_560   12.01100  ; C4  in imidazole
>  opls_561   12.01100  ; C5  in imidazole
>  opls_562    1.00800  ; H1  in imidazole
>  opls_563    1.00800  ; H2  in imidazole
>  opls_564    1.00800  ; H4  in imidazole
>  opls_565    1.00800  ; H5  in imidazole
> 
> But there are no parameters for these atoms in the ffoplsaa.rtp file. 
> Does anyone know how I can go about naming these atoms in my pdb file? 
> Thank you in advance.
> 

Not every compound is present in a .rtp file.  Check out its contents and you'll 
see what it has - pretty much just amino acids.  The charges on each atom are 
not specific to an atom type, they are specific to a chemical species for which 
the parameterization scheme has been conducted.  Lennard-Jones parameters are 
specified in ffoplsaanb.itp.

I suggest a thorough read of Chapter 5 of the manual to understand the contents 
of these database-type files, and how they are used in assembling a topology.

-Justin

> Jacob Harvey
> 
> -- 
> --
> Jacob Harvey
> 
> Graduate Student
> 
> University of Massachusetts Amherst
> 
> j.harv8 at gmail.com <mailto:j.harv8 at gmail.com>
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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