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
--
========================================
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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