[gmx-users] adding a new residue in the ff

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 31 19:27:17 CEST 2011


> It would probably be easier, faster, and more accurate to just use most of
> the parameters for Cys rather than try to have PRODRG re-create a
> (potentially flawed) model of your compound.  The only new parameters are
> related to SO3, so the rest should be identical to the Cys residue.

That's not a good idea. It'll only do for the backbone. The charge of
CB will be quite different, as well as the CA-CB-SG angle, and for the
rest there's nothing similar even.

> This is where parameterization becomes a chore - when there's nothing
> analogous to what you're doing.  Proper Gromos96 parameterization
> methodology would dictate that you generate an analogous compound (i.e.,
> methyl sulfonic acid) and adjust its parameters such that it reproduces
> various condensed-phase thermodynamic and physical properties (DeltaG of
> solvation, liquid density, heat of vaporization).  Proper derivation is
> quite time-consuming.  Perhaps someone has already done this work and it is
> published.  If you're unlucky, you've got to do it all yourself.

That's a good idea :)



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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