AMBER Archive (2008)

Subject: Re: AMBER: a question about ff03ua

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Dec 25 2008 - 15:01:56 CST

On Thu, Dec 25, 2008, oguz gurbulak wrote:
>
> I
> tried to prepare a structure to get the prmtop and inpcrd input files
> for ff03ua force field. And I did all the operations in below. But
> after I got the frcmod file , I realized that there are some AA force
> field parameters in it. So I thougt that I didn't / couldn't generate
> a UA prepin file for my MD simulations.

Antechamber inherently works in an all-atom environment. You can't use
it to generate united atom parameters.

It's not even clear what would qualify as a "ff03ua" force field for
octane: ff03ua was parameterized for amino acids, and it is not clear
(to me) that there exists a systematic procedure for generating the UA
forcefield for arbitrary molecules.

For octane, you might try this: generate a mol2 file by hand, with the
same carbon paramters used for aliphatic side chains. All the charges
will be zero (more or less required). This should get you something
compatible with ff03ua -- no guarantees at all about comparison to
experiment! You might also see what something like opls/ua has done for
alkanes.

...good luck...dac

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