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

[Justin A. Lemkul]

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...

-Justin

>> 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
> 
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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