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

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 31 19:29:54 CEST 2011

Tsjerk Wassenaar wrote:
> Hi,
>> 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.

Gah, that's what I meant.  Thanks for pointing that out!  I guess I've stated so 
many times (and published on the fact) that PRODRG charges are useless that I'm 
no longer even quoting myself...


>> 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 :)
> Cheers,
> Tsjerk


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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