[gmx-users] oxaloacetate and atp

[Justin A. Lemkul]

Quoting "E.M." <pckboy at gmail.com>:

> Greetings.
>
> I was wondering if any of you have a library file for oxaloacetate
> compatible with
> the atp files of any force field?.  Your quick input would be greatly
> appreciated,
> also I was wondering, how to include these not standard molecules so I can
> create an initial system?.

Parameters for ATP have already been derived and are included in the Gromos96
force fields.  Check the .rtp files, and you will find ATP.  As for
oxaloacetate, you will likely have to derive parameters for them yourself,
which is an advanced topic and should not be taken lightly.  You would have to
derive these parameters in a manner consistent with the derivation of the
original force field.

See here: http://wiki.gromacs.org/index.php/Parameterization

As for including these parameters, search the manual for information about
topologies, especially .itp files.

-Justin

>
>
> Thanks for the help
>
> Eduard
>
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========================================

Justin A. Lemkul
Graduate Research Assistant
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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