[gmx-users] adding dithiothreitol to amber03

[Mark Abraham]

Hi,

You can't blindly mix and match parameters for different force fields and
hope to get a valid model. See
http://www.gromacs.org/Documentation/How-tos/Parameterization for tips. As
a bonus, tools that help derive parameters for AMBER force fields will tend
to produce output files that can be converted to GROMACS formats readily.
For setting up an input structure, the ideas at
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents are useful -
start with protein and treat DTT as a co-solvent.

Mark

On Mon, Oct 24, 2016 at 5:51 PM Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> I am trying to add the parameters for dithiothreitol (DTT) to the amber03
> force field. My system will have a protein solvated in a box containing a
> few DTT molecules. I've found parameters for Gromacs, but for the Gromos
> 54A7 force field. How can I modify the amber03 files to add this molecule?
> Would it be possible to treat this as an ion so that it can be added to the
> box with gmx genion?
>
> Best,
> Irem
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