Dear Justin
Parameterization is a tough task, if done properly. If you find it
came easy, it's probably not right ;) It sounds like you're trying to
work backwards from PRODRG and correct the charges. While that can be
OK, if you've committed to using the Gromos96 force fields, I'd
suggest you work the other way around. Look into the literature and
see if anyone else has done anything similar - what force field did
they use? Was it successful? Frankly, the details of parameterization
for Amber, CHARMM, and OPLS are significantly more detailed than those
of the Gromos96 force fields, so you may actually find it easier to
use the QM methods described for those other force fields. The next
most significant issue is validation. You have to have some criteria
by which your new parameters are judged. Again, this is a reason why
Gromos96 can be tough, unless you have DeltaG of solvation for your
compounds, or suitable models thereof. There are alternatives, but
they're not significantly better. Reproducing some condensed-phase
criteria is common to all the force fields (some have additional QM
geometry requirements).
Many thanks for the detailed response; I really appreciate it. I've
enjoyed reading the papers you've contributed to.
I'm not really tied in with any particular force fields at the moment,
and I am teaching myself how to use AMBER, which admittedly does seem to
be a lot more amenable to novel 'residues', what with the GAFF. I
haven't been able to find any parameters which people have used for
phosphate esters in the literature, though as I said there's an
abundance of them for phospholipids. The real problem is that I don't
have enough experience to say that parameters relating to groups which
appear in my molecules as well as, say, DPPC (e.g. PO4) are going to be
similar enough. I will take your advice though and continue searching (I
haven't been able to have a look at Lipidbook yet actually, but have
e-mailed Professor Mark Sansom and he's said they're having server
problems and hope to be back soon), and will start using AMBER in more
earnest.
Best regards
Ben
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